TEMP

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hello ive tried the TEMP_absence.sh (`bash ../scripts/TEMP_Absence.sh -i ./test_chromosome.sorted.bam -s ../scripts -r ./test_TE_annotation.bed -t ./dm3_chr2L.2bit)` on test data and i got this error **Error: Type checker found wrong number of...

rachidelfermi

TEMP_insertion returns no input. I have tried to run it with parameters similar to other contributors in the thread below this. However, it still does not work. Has there been...

CGNAT

TEMP_Insertion.sh produces empty output

5

Hi Jiali, I'm having some trouble getting TEMP to work properly. Most of the output files that are produced are empty (or empty except for the headers). No error messages...

davidecarlson

Error when running TEMP

7

Hi, I get this error when running "TEMP_Insertion.sh": ERROR: Received illegal bin number 262143 from getBin call. ERROR: Unable to add record to tree. Possible reason for causing this? Best,...

simoncchu

Invalid record in bam.unproper.uniq.interval.bed

3

Hi, I get this error when running "TEMP_Absence.sh": ``` bedtools intersect -a /cluster/project/gdc/people/crimjhim/TEPID_final.bed.sort -b merged.Ma99.bam.unproper.uniq.interval.bed -f 1.0 -wo Error: Invalid record in file merged.Ma99.bam.unproper.uniq.interval.bed. Record is chr1 2287009 2287008 HWI-700523F:21:C6KJ9ANXX:4:2301:14610:90784/2...

rimjhimroy

no output with either test data or my own data

1

I debugged and it seems to be an samtools problem, everything run fine till samtools kicks in. the test data would go through the whole process. I cannt seem to...

hshcao

view: invalid option -- 'X'

1

Hi, I have got a failure information (view: invalid option -- 'X') while running your TEMP on your small test data. It looks like the error comes from Samtools, because...

taozuo16

I'd like to request that you tag a TEMP release so that we can be sure that we're always using the same version of TEMP.

mes5k

BWA version

3

Hi, I have noticed some issues when trying to run your software. It seems that you rely on using the old version of bwa (pre. 0.7) to run the pipeline...

nelson42

girmab