Anna-Leigh Brown
The tags looks something like this: ``` A00420:310:HWVTKDMXX:2:2164:6262:32784 419 chr1 14442 1 56M = 14442 0 TCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF AS:i:0 NH:i:3 XM:i:0 NM:i:0 MD:Z:56 YS:i:0 YZ:A:+ Yf:i:0 ZS:i:0 XN:i:0 XO:i:0 XG:i:0...
Just following up, I've about got a script which could add on the RA and MP:Z tags to a HISAT3N aligned bam Just perusing the tags on some bams I...
Yep! I've read that supplement, but if you see the MP tags produced by NGM e.g. MP:Z:2:38:38,16:70:70,10:80:80,7:110:110,10:189:189,16:202:202 How does a reference position of 38 follow? As a guess, I'm going...
Install works -- leaving issue open as the docs are still incorrect
Actually I ammend this; Based on troubles I'm having reading BAM files, I think installing directly with homebrew does not correctly link against zlib.h https://github.com/seqan/seqan/issues/2056
Same issue here with paired-end reads. `ERROR: LoadError: BoundsError: attempt to access 1-element Array{Whippet.SGAlignNode,1} at index [3] Stacktrace:` built the index using a bam file; but in our use case...
The other possibility here would be using Cufflinks or Stringtie to make a merged gtf that includes the novel transcripts found in the bams and then building a Whippets index...
For what it's worth, I've had some success using MAJIQ on our data set, but that's only 30 + samples, caveat that their outputs are more difficult to interpret than...
Might want to stop clogging this Github issue on this point since it's not Whippets issue per se; feel free to email or twitter DM on it
Also exploring the probability distributions with `modkit sample-probs` - here I'm just showing the cumulative probability for our 2 conditions, 3 samples each, and there's a systemic difference between our...