split gamp by chromosome or extract specific regions.
Hi,
I am trying to run transcriptome analysis, but RPVG is failing. I suspect this could be due to some issues with tangled graphs, so I am attempting to run RPVG by chromosome or by using specific regions. However, I am unable to figure out how to split the GAMP file or extract specific regions from it. Could you please guide me on how to do that?
Thank you in advance for your help!
• 779 views
•
link
updated
by
Jordan M Eizenga •
•
written
by
Juhyun •
•
written
by
Juhyun •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Reference VCF with "chr" contigs instead of "number"
written by GPR
-
Issues adding GTF track to split genome on IGV
written by Daisy •
-
PopGenome stats for each population
written by Yixuan •
-
vg mpmap(multi-map across other regions?)
written by Juhyun •
-
Compute matrix skipping many regions stating not found in compute matrix output
written by mavy •
-
Construct a pantranscriptome reference with two haplotypes from a single sample.
written by Juhyun •
-
samtools view extract from .bed list to .bam file
written by matthews.alix •
-
Maker annotation speed up
written by ambedoya •
-
How to get a list of snp associated with any known cancer from NCBI with chromosomal locations?
written by mrj •
-
How to extract chrX, chrY and chrM from a vcf file?
written by MAPK
As of this moment, there's not a very direct way to do this. With GAM files, it's possible to use
vg annotate -bfollowed byvg filter -U -F. For a GAMP file, you could convert to a GAM and then do this process, but the conversion is lossy. However, you could extract the read names and then usevg filter -M -N.