why the bed produced by bowtie2 and tophat2 are different?

Question

[zizigolu]

Hi friends,

My accepted_hits.bam produced by tophat2 is different from bed produced by bowtie2 because is has not gene name in column one anymore and when I tried to extract the average of reads by biophysconnector package it told:

> source('/usr/data/nfs6/izadi/dropoff_matrix_modified_Subramaniam_yesleu.R')
Error in `colnames<-`(`*tmp*`, value = c("Gene ID", "Gene length", "Gene ID",  :
  length of 'dimnames' [2] not equal to array extent

What can I do to have a bed but hasing the gene name in column one please?

Answer 1

[Devon Ryan]

Bowtie2 doesn't produce BED files, presumably you meant a BAM file. In any case, I wouldn't expect a splicing-aware aligner to produce the same output as an unspliced aligner (there is no reason to use bowtie2 when aligning RNAseq reads unless you're aligning directly against the transcriptome).

SInce we can't see the contents of the .R file, there's no possible way we could help at all. In any case, try to figure out what that error means and run the .R file line by line so you know exactly what line causes it (if you don't already know).

[zizigolu]

thank you Devon