Average read length by position BAM file
Hello everyone! Is there a tool which can be used to extract the average length of mapped reads in each position per chromosome? Thanks in advance!
• 1,088 views
•
link
updated
by
ATpoint
•
written
by
mmarcell •
•
written
by
mmarcell •
1 answer
it sounds like a XY problem. What's the point of this ?
Anyway, using bioalcidaejdk http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html and datamash:
java -jar ${JVARKIT_DIST}/bioalcidaejdk.jar -e 'stream().forEach(R->println(R.getContig()+":"+R.getStart()+"\t"+R.getReadLength()));' coord.sorted.bam | datamash -g 1 mean 2
(...)
RF01:1 70
RF01:8 70
RF01:11 70
RF01:12 70
RF01:27 70
RF01:44 70
RF01:67 70
RF01:94 70
RF01:102 70
RF01:110 70
• 0 views
•
link
written
by
Pierre Lindenbaum
Log in to answer this question.
More posts like this
-
Filteration of uniquely mapped reads
written by Omics data mining
-
Splitting VCF into 10mb window subfiles for a given chromosome
written by ThunderPhoenix •
-
Extract 'endpos' feature from bam file
written by qstefano •
-
Average Read length
written by serene.s •
-
Convert a VCF-file in a user specific Format
written by dominik.lagler •
-
Get per-nucleotide mapping position for each mapped reads from bam file
written by Changhao Li •
-
Merge STAR Log.final.out files together
written by minifoog •
-
Is it possible to pool the paired-end data?
written by tanya_fiskur •
-
Terrible RNA mapping result by STAR
written by 610225668 •
-
Non-Redundant Data Sets Of Protein
written by eka0700 •
May I ask what this would be useful for. No, probably no out-of-the-box tool. There are many posts on biostars on extracting read length from a BAM. It will be tedious as you describe it. Do you really need every genome position? For human that will be three billion "average read lengths".