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Issue with Running Differential Analysis
Dear Suppa Members I am having some trouble while running differential analysis with local events and isoforms. Any help will be appreciated.
I am running this script for the local events
for f in /staton/projects/alternative_splicing/prunus_persica/combined/7_splice_events/*.ioe
do
base=$(basename $f | sed 's/.ioe//g')
echo "filename $f base $base"
suppa.py diffSplice --method empirical --input $f --psi /staton/projects/alternative_splicing/prunus_persica/dormancy/7_splice_events/$base.event.psi /staton/projects/alternative_splicing/prunus_persica/flower/7_splice_events/$base.event.psi --tpm /staton/projects/alternative_splicing/prunus_persica/dormancy/normalized_counts/peach1_normalized_bud.txt /staton/projects/alternative_splicing/prunus_persica./flower/normalized_counts/peach1_normalized_bud.txt --area 1000 --lower-bound 0.05 -gc -o $base.BudvsFlower.delta.psi
done
And I keep getting this error
ERROR:__main__:Unknown error: (<class 'IndexError'>, IndexError('list index out of range'), <traceback object at 0x7f33d24366e0>)
These are the first few lines of my input files
ioe files
seqname gene_id event_id alternative_transcripts total_transcripts
Pp01 MSTRG.18 MSTRG.18;AL:Pp01:231534-232036:232151:231534-232611:233106:+ Prupe.1G002100.1_v2.0.a1,Prupe.1G002100.5_v2.0.a1 Prupe.1G002100.4_v2.0.a1,Prupe.1G002100.2_v2.0.a1,Prupe.1G002100.5_v2.0.a1,Prupe.1G002100.1_v2.0.a1,Prupe.1G002100.3_v2.0.a1
Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-689219:689443:687149-689702:689706:+ Prupe.1G008200.4_v2.0.a1 Prupe.1G008200.4_v2.0.a1,Prupe.1G008200.2_v2.0.a1
Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-688946:689443:687149-689702:689706:+ Prupe.1G008200.3_v2.0.a1 Prupe.1G008200.3_v2.0.a1,Prupe.1G008200.2_v2.0.a1
Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-689185:689443:687149-689702:689706:+ Prupe.1G008200.6_v2.0.a1 Prupe.1G008200.6_v2.0.a1,Prupe.1G008200.2_v2.0.a1
Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-687892:689443:687149-689702:689706:+ Prupe.1G008200.5_v2.0.a1 Prupe.1G008200.5_v2.0.a1,Prupe.1G008200.2_v2.0.a1
Pp01 MSTRG.68 MSTRG.68;AL:Pp01:713853-714460:715134:713853-716070:716872:+ Prupe.1G008700.4_v2.0.a1 Prupe.1G008700.3_v2.0.a1,Prupe.1G008700.4_v2.0.a1,Prupe.1G008700.1_v2.0.a1,Prupe.1G008700.2_v2.0.a1
Pp01 MSTRG.285 MSTRG.285;AL:Pp01:3019463-3019771:3020203:3019463-3020401:3020466:+ Prupe.1G042300.3_v2.0.a1 Prupe.1G042300.2_v2.0.a1,Prupe.1G042300.3_v2.0.a1
Pp01 MSTRG.443 MSTRG.443;AL:Pp01:5043344-5043696:5043756:5043344-5044155:5044492:+ Prupe.1G071200.3_v2.0.a1,Prupe.1G071200.4_v2.0.a1 Prupe.1G071200.4_v2.0.a1,Prupe.1G071200.2_v2.0.a1,Prupe.1G071200.3_v2.0.a1,Prupe.1G071200.1_v2.0.a1
Pp01 MSTRG.701 MSTRG.701;AL:Pp01:8850866-8850990:8851101:8850866-8851102:8851668:+ Prupe.1G110700.6_v2.0.a1,Prupe.1G110700.7_v2.0.a1 Prupe.1G110700.1_v2.0.a1,Prupe.1G110700.6_v2.0.a1,Prupe.1G110700.4_v2.0.a1,Prupe.1G110700.7_v2.0.a1,Prupe.1G110700.5_v2.0.a1,Prupe.1G110700.3_v2.0.a1
PSI
T3.1 T3.2 T3.3
MSTRG.1001;AL:Pp01:12086853-12087221:12087253:12086853-12087475:12088133:+ 0.001687486073377343 0.0013726115391085876 3.752431388073356e-05
MSTRG.10030;AL:Pp04:15801659-15802469:15802852:15801659-15804387:15804526:+ 1.0 0.9435237096070532 0.9996908348433943
MSTRG.10036;AL:Pp04:15953549:15954018-15954372:15954099:15954173-15954372:- 0.9986609931131296 0.9970137910879916 0.9970650029033897
MSTRG.10048;AL:Pp04:16074963:16075752-16076441:16075994:16076362-16076441:- 0.9708592662889681 1.0 0.887998991355499
MSTRG.10048;AL:Pp04:16075116:16075752-16076441:16075994:16076362-16076441:- 0.5135212096095823 1.0 0.8753171260567173
MSTRG.10048;AL:Pp04:16075119:16075752-16076441:16075994:16076362-16076441:- 0.9370065327293955 1.0 0.0006364631300304236
MSTRG.10107;AL:Pp04:17591814-17592016:17592322:17591814-17592410:17593078:+ 0.025145150954209383 0.04980099880488245 0.06969539905231396
MSTRG.10140;AL:Pp04:18581768:18582561-18583621:18582955:18583478-18583621:- 1.0 1.1361090050889003e-17 1.3517934217620798e-15
MSTRG.10140;AL:Pp04:18581768:18582610-18583621:18582955:18583478-18583621:- 1.0 1.1361090050889003e-17 1.3517934217620798e-15
Normalized Counts
T3.1 T3.2 T3.3
Prupe.2G003500.1_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17
Prupe.6G168600.8_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17
Prupe.1G068900.1_v2.0.a1 20.1620932023874 0 0.0589230568340313
Prupe.3G187500.8_v2.0.a1 2.16949418439215 0 0.0268398490729202
Prupe.6G316500.4_v2.0.a1 0 128.418207964263 0.0672456383365763
Prupe.8G189100.2_v2.0.a1 0 0 17.7802104695726
Prupe.4G233900.1_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17
Prupe.2G194000.1_v2.0.a1 10.3294207260643 9.93181059468324 0.0590991047951266
Prupe.3G173900.2_v2.0.a1 25.3893952210739 27.9574655866061 9.09680849403876
Hi,
I am wondering, is suppa.py in your path? Your command does not call python. It could also be that it is not using python3.4?
The input files seem ok.
The expression files, is it TPMs or normalised counts?
Thanks
Eduardo
On Sat, 24 Oct 2020 at 05:16, RaymondS1 [email protected] wrote:
These are the first few lines of my input files
ioe files
seqname gene_id event_id alternative_transcripts total_transcripts Pp01 MSTRG.18 MSTRG.18;AL:Pp01:231534-232036:232151:231534-232611:233106:+ Prupe.1G002100.1_v2.0.a1,Prupe.1G002100.5_v2.0.a1 Prupe.1G002100.4_v2.0.a1,Prupe.1G002100.2_v2.0.a1,Prupe.1G002100.5_v2.0.a1,Prupe.1G002100.1_v2.0.a1,Prupe.1G002100.3_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-689219:689443:687149-689702:689706:+ Prupe.1G008200.4_v2.0.a1 Prupe.1G008200.4_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-688946:689443:687149-689702:689706:+ Prupe.1G008200.3_v2.0.a1 Prupe.1G008200.3_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-689185:689443:687149-689702:689706:+ Prupe.1G008200.6_v2.0.a1 Prupe.1G008200.6_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-687892:689443:687149-689702:689706:+ Prupe.1G008200.5_v2.0.a1 Prupe.1G008200.5_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.68 MSTRG.68;AL:Pp01:713853-714460:715134:713853-716070:716872:+ Prupe.1G008700.4_v2.0.a1 Prupe.1G008700.3_v2.0.a1,Prupe.1G008700.4_v2.0.a1,Prupe.1G008700.1_v2.0.a1,Prupe.1G008700.2_v2.0.a1 Pp01 MSTRG.285 MSTRG.285;AL:Pp01:3019463-3019771:3020203:3019463-3020401:3020466:+ Prupe.1G042300.3_v2.0.a1 Prupe.1G042300.2_v2.0.a1,Prupe.1G042300.3_v2.0.a1 Pp01 MSTRG.443 MSTRG.443;AL:Pp01:5043344-5043696:5043756:5043344-5044155:5044492:+ Prupe.1G071200.3_v2.0.a1,Prupe.1G071200.4_v2.0.a1 Prupe.1G071200.4_v2.0.a1,Prupe.1G071200.2_v2.0.a1,Prupe.1G071200.3_v2.0.a1,Prupe.1G071200.1_v2.0.a1 Pp01 MSTRG.701 MSTRG.701;AL:Pp01:8850866-8850990:8851101:8850866-8851102:8851668:+ Prupe.1G110700.6_v2.0.a1,Prupe.1G110700.7_v2.0.a1 Prupe.1G110700.1_v2.0.a1,Prupe.1G110700.6_v2.0.a1,Prupe.1G110700.4_v2.0.a1,Prupe.1G110700.7_v2.0.a1,Prupe.1G110700.5_v2.0.a1,Prupe.1G110700.3_v2.0.a1
PSI
T3.1 T3.2 T3.3 MSTRG.1001;AL:Pp01:12086853-12087221:12087253:12086853-12087475:12088133:+ 0.001687486073377343 0.0013726115391085876 3.752431388073356e-05 MSTRG.10030;AL:Pp04:15801659-15802469:15802852:15801659-15804387:15804526:+ 1.0 0.9435237096070532 0.9996908348433943 MSTRG.10036;AL:Pp04:15953549:15954018-15954372:15954099:15954173-15954372:- 0.9986609931131296 0.9970137910879916 0.9970650029033897 MSTRG.10048;AL:Pp04:16074963:16075752-16076441:16075994:16076362-16076441:- 0.9708592662889681 1.0 0.887998991355499 MSTRG.10048;AL:Pp04:16075116:16075752-16076441:16075994:16076362-16076441:- 0.5135212096095823 1.0 0.8753171260567173 MSTRG.10048;AL:Pp04:16075119:16075752-16076441:16075994:16076362-16076441:- 0.9370065327293955 1.0 0.0006364631300304236 MSTRG.10107;AL:Pp04:17591814-17592016:17592322:17591814-17592410:17593078:+ 0.025145150954209383 0.04980099880488245 0.06969539905231396 MSTRG.10140;AL:Pp04:18581768:18582561-18583621:18582955:18583478-18583621:- 1.0 1.1361090050889003e-17 1.3517934217620798e-15 MSTRG.10140;AL:Pp04:18581768:18582610-18583621:18582955:18583478-18583621:- 1.0 1.1361090050889003e-17 1.3517934217620798e-15
Normalized Counts
T3.1 T3.2 T3.3 Prupe.2G003500.1_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17 Prupe.6G168600.8_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17 Prupe.1G068900.1_v2.0.a1 20.1620932023874 0 0.0589230568340313 Prupe.3G187500.8_v2.0.a1 2.16949418439215 0 0.0268398490729202 Prupe.6G316500.4_v2.0.a1 0 128.418207964263 0.0672456383365763 Prupe.8G189100.2_v2.0.a1 0 0 17.7802104695726 Prupe.4G233900.1_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17 Prupe.2G194000.1_v2.0.a1 10.3294207260643 9.93181059468324 0.0590991047951266 Prupe.3G173900.2_v2.0.a1 25.3893952210739 27.9574655866061 9.09680849403876
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-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ
Hello Eduardo, Thank you for your response @EduEyras. Suppa.py is listed in the path and the bash command calls on python 3.4. But the error still persists. Also, the expression files are normalized counts.
Please let me know if you have any other ideas as to the error is from. -Raymond
Hi, I am wondering, is suppa.py in your path? Your command does not call python. It could also be that it is not using python3.4? The input files seem ok. The expression files, is it TPMs or normalised counts? Thanks Eduardo … On Sat, 24 Oct 2020 at 05:16, RaymondS1 @.***> wrote: These are the first few lines of my input files ioe files seqname gene_id event_id alternative_transcripts total_transcripts Pp01 MSTRG.18 MSTRG.18;AL:Pp01:231534-232036:232151:231534-232611:233106:+ Prupe.1G002100.1_v2.0.a1,Prupe.1G002100.5_v2.0.a1 Prupe.1G002100.4_v2.0.a1,Prupe.1G002100.2_v2.0.a1,Prupe.1G002100.5_v2.0.a1,Prupe.1G002100.1_v2.0.a1,Prupe.1G002100.3_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-689219:689443:687149-689702:689706:+ Prupe.1G008200.4_v2.0.a1 Prupe.1G008200.4_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-688946:689443:687149-689702:689706:+ Prupe.1G008200.3_v2.0.a1 Prupe.1G008200.3_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-689185:689443:687149-689702:689706:+ Prupe.1G008200.6_v2.0.a1 Prupe.1G008200.6_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-687892:689443:687149-689702:689706:+ Prupe.1G008200.5_v2.0.a1 Prupe.1G008200.5_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.68 MSTRG.68;AL:Pp01:713853-714460:715134:713853-716070:716872:+ Prupe.1G008700.4_v2.0.a1 Prupe.1G008700.3_v2.0.a1,Prupe.1G008700.4_v2.0.a1,Prupe.1G008700.1_v2.0.a1,Prupe.1G008700.2_v2.0.a1 Pp01 MSTRG.285 MSTRG.285;AL:Pp01:3019463-3019771:3020203:3019463-3020401:3020466:+ Prupe.1G042300.3_v2.0.a1 Prupe.1G042300.2_v2.0.a1,Prupe.1G042300.3_v2.0.a1 Pp01 MSTRG.443 MSTRG.443;AL:Pp01:5043344-5043696:5043756:5043344-5044155:5044492:+ Prupe.1G071200.3_v2.0.a1,Prupe.1G071200.4_v2.0.a1 Prupe.1G071200.4_v2.0.a1,Prupe.1G071200.2_v2.0.a1,Prupe.1G071200.3_v2.0.a1,Prupe.1G071200.1_v2.0.a1 Pp01 MSTRG.701 MSTRG.701;AL:Pp01:8850866-8850990:8851101:8850866-8851102:8851668:+ Prupe.1G110700.6_v2.0.a1,Prupe.1G110700.7_v2.0.a1 Prupe.1G110700.1_v2.0.a1,Prupe.1G110700.6_v2.0.a1,Prupe.1G110700.4_v2.0.a1,Prupe.1G110700.7_v2.0.a1,Prupe.1G110700.5_v2.0.a1,Prupe.1G110700.3_v2.0.a1 PSI T3.1 T3.2 T3.3 MSTRG.1001;AL:Pp01:12086853-12087221:12087253:12086853-12087475:12088133:+ 0.001687486073377343 0.0013726115391085876 3.752431388073356e-05 MSTRG.10030;AL:Pp04:15801659-15802469:15802852:15801659-15804387:15804526:+ 1.0 0.9435237096070532 0.9996908348433943 MSTRG.10036;AL:Pp04:15953549:15954018-15954372:15954099:15954173-15954372:- 0.9986609931131296 0.9970137910879916 0.9970650029033897 MSTRG.10048;AL:Pp04:16074963:16075752-16076441:16075994:16076362-16076441:- 0.9708592662889681 1.0 0.887998991355499 MSTRG.10048;AL:Pp04:16075116:16075752-16076441:16075994:16076362-16076441:- 0.5135212096095823 1.0 0.8753171260567173 MSTRG.10048;AL:Pp04:16075119:16075752-16076441:16075994:16076362-16076441:- 0.9370065327293955 1.0 0.0006364631300304236 MSTRG.10107;AL:Pp04:17591814-17592016:17592322:17591814-17592410:17593078:+ 0.025145150954209383 0.04980099880488245 0.06969539905231396 MSTRG.10140;AL:Pp04:18581768:18582561-18583621:18582955:18583478-18583621:- 1.0 1.1361090050889003e-17 1.3517934217620798e-15 MSTRG.10140;AL:Pp04:18581768:18582610-18583621:18582955:18583478-18583621:- 1.0 1.1361090050889003e-17 1.3517934217620798e-15 Normalized Counts T3.1 T3.2 T3.3 Prupe.2G003500.1_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17 Prupe.6G168600.8_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17 Prupe.1G068900.1_v2.0.a1 20.1620932023874 0 0.0589230568340313 Prupe.3G187500.8_v2.0.a1 2.16949418439215 0 0.0268398490729202 Prupe.6G316500.4_v2.0.a1 0 128.418207964263 0.0672456383365763 Prupe.8G189100.2_v2.0.a1 0 0 17.7802104695726 Prupe.4G233900.1_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17 Prupe.2G194000.1_v2.0.a1 10.3294207260643 9.93181059468324 0.0590991047951266 Prupe.3G173900.2_v2.0.a1 25.3893952210739 27.9574655866061 9.09680849403876 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#104 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7WHEAVBA6KOGGG4KLSMHCBBANCNFSM4S43YWEA . -- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ
Hi,
If you run each command separately, outside the bash loop, do you get the same error for all $base and $f files? Or for some of them?
That error tends to appear when there is an issue with the labels of the samples. For instance, it reads 4 columns instead of three due to some extra "\t" character, and then it is expecting four data columns in the rest of the file.
If both conditions have the same column IDs, that might cause some trouble as well.
On an unrelated matter. I am not sure whether normalised counts will be valid to calculate PSIs, since they are not normalised for length. You do get some number, between 0 and 1 because how the PSI is calculated, but we have not benchmarked that number vs RT-PCR or junction-based analyses. So I don't know whether that would be correct.
I hope this helps. Please let me know how it goes Thanks
Eduardo
On Thu, 29 Oct 2020 at 01:35, RaymondS1 [email protected] wrote:
Hello Eduardo, Thank you for your response. Suppa.py is listed in the path and the bash command calls on python 3.4. But the error still persists. Also, the expression files are normalized counts.
Please let me know if you have any other ideas as to the error is from. -Raymond
Hi, I am wondering, is suppa.py in your path? Your command does not call python. It could also be that it is not using python3.4? The input files seem ok. The expression files, is it TPMs or normalised counts? Thanks Eduardo … <#m_2688419067343636096_> On Sat, 24 Oct 2020 at 05:16, RaymondS1 @.***> wrote: These are the first few lines of my input files ioe files seqname gene_id event_id alternative_transcripts total_transcripts Pp01 MSTRG.18 MSTRG.18;AL:Pp01:231534-232036:232151:231534-232611:233106:+ Prupe.1G002100.1_v2.0.a1,Prupe.1G002100.5_v2.0.a1 Prupe.1G002100.4_v2.0.a1,Prupe.1G002100.2_v2.0.a1,Prupe.1G002100.5_v2.0.a1,Prupe.1G002100.1_v2.0.a1,Prupe.1G002100.3_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-689219:689443:687149-689702:689706:+ Prupe.1G008200.4_v2.0.a1 Prupe.1G008200.4_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-688946:689443:687149-689702:689706:+ Prupe.1G008200.3_v2.0.a1 Prupe.1G008200.3_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-689185:689443:687149-689702:689706:+ Prupe.1G008200.6_v2.0.a1 Prupe.1G008200.6_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.66 MSTRG.66;AL:Pp01:687149-687892:689443:687149-689702:689706:+ Prupe.1G008200.5_v2.0.a1 Prupe.1G008200.5_v2.0.a1,Prupe.1G008200.2_v2.0.a1 Pp01 MSTRG.68 MSTRG.68;AL:Pp01:713853-714460:715134:713853-716070:716872:+ Prupe.1G008700.4_v2.0.a1 Prupe.1G008700.3_v2.0.a1,Prupe.1G008700.4_v2.0.a1,Prupe.1G008700.1_v2.0.a1,Prupe.1G008700.2_v2.0.a1 Pp01 MSTRG.285 MSTRG.285;AL:Pp01:3019463-3019771:3020203:3019463-3020401:3020466:+ Prupe.1G042300.3_v2.0.a1 Prupe.1G042300.2_v2.0.a1,Prupe.1G042300.3_v2.0.a1 Pp01 MSTRG.443 MSTRG.443;AL:Pp01:5043344-5043696:5043756:5043344-5044155:5044492:+ Prupe.1G071200.3_v2.0.a1,Prupe.1G071200.4_v2.0.a1 Prupe.1G071200.4_v2.0.a1,Prupe.1G071200.2_v2.0.a1,Prupe.1G071200.3_v2.0.a1,Prupe.1G071200.1_v2.0.a1 Pp01 MSTRG.701 MSTRG.701;AL:Pp01:8850866-8850990:8851101:8850866-8851102:8851668:+ Prupe.1G110700.6_v2.0.a1,Prupe.1G110700.7_v2.0.a1 Prupe.1G110700.1_v2.0.a1,Prupe.1G110700.6_v2.0.a1,Prupe.1G110700.4_v2.0.a1,Prupe.1G110700.7_v2.0.a1,Prupe.1G110700.5_v2.0.a1,Prupe.1G110700.3_v2.0.a1 PSI T3.1 T3.2 T3.3 MSTRG.1001;AL:Pp01:12086853-12087221:12087253:12086853-12087475:12088133:+ 0.001687486073377343 0.0013726115391085876 3.752431388073356e-05 MSTRG.10030;AL:Pp04:15801659-15802469:15802852:15801659-15804387:15804526:+ 1.0 0.9435237096070532 0.9996908348433943 MSTRG.10036;AL:Pp04:15953549:15954018-15954372:15954099:15954173-15954372:- 0.9986609931131296 0.9970137910879916 0.9970650029033897 MSTRG.10048;AL:Pp04:16074963:16075752-16076441:16075994:16076362-16076441:- 0.9708592662889681 1.0 0.887998991355499 MSTRG.10048;AL:Pp04:16075116:16075752-16076441:16075994:16076362-16076441:- 0.5135212096095823 1.0 0.8753171260567173 MSTRG.10048;AL:Pp04:16075119:16075752-16076441:16075994:16076362-16076441:- 0.9370065327293955 1.0 0.0006364631300304236 MSTRG.10107;AL:Pp04:17591814-17592016:17592322:17591814-17592410:17593078:+ 0.025145150954209383 0.04980099880488245 0.06969539905231396 MSTRG.10140;AL:Pp04:18581768:18582561-18583621:18582955:18583478-18583621:- 1.0 1.1361090050889003e-17 1.3517934217620798e-15 MSTRG.10140;AL:Pp04:18581768:18582610-18583621:18582955:18583478-18583621:- 1.0 1.1361090050889003e-17 1.3517934217620798e-15 Normalized Counts T3.1 T3.2 T3.3 Prupe.2G003500.1_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17 Prupe.6G168600.8_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17 Prupe.1G068900.1_v2.0.a1 20.1620932023874 0 0.0589230568340313 Prupe.3G187500.8_v2.0.a1 2.16949418439215 0 0.0268398490729202 Prupe.6G316500.4_v2.0.a1 0 128.418207964263 0.0672456383365763 Prupe.8G189100.2_v2.0.a1 0 0 17.7802104695726 Prupe.4G233900.1_v2.0.a1 5.55111512312578e-17 5.55111512312578e-17 5.55111512312578e-17 Prupe.2G194000.1_v2.0.a1 10.3294207260643 9.93181059468324 0.0590991047951266 Prupe.3G173900.2_v2.0.a1 25.3893952210739 27.9574655866061 9.09680849403876 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#104 (comment) https://github.com/comprna/SUPPA/issues/104#issuecomment-715499205>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7WHEAVBA6KOGGG4KLSMHCBBANCNFSM4S43YWEA . -- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ
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