count of reads having multiple references

Question

[vmicrobio]

Hi all,

I have done an alignment using bwa on numerous references and I would like to retrieve a count of the reads matching more than one references and know witch references are involved.

This question is related to this post : How to highlight multiple references mapped reads?, but here I don't need to get reads, only a count. I also would like to answer it differently because in my case it makes samtools stop the process for some samples

Thanks a lot!

[Pierre Lindenbaum]

but here I don't need to get reads, only a count

wc is your friend

because in my case it makes samtools stop the process for some samples

why ? show us the error

[vmicrobio]

Yes wc is definitively what I need to count

Here is the error (certainly due to a lack of computing power, because it works for some of my files and I couldn't detect any corrupted files):

auto.sh : ligne 7 :  4800 Relais brisé (pipe)    samtools view file55-sorted.bam
      4801 Processus arrêté      | grep -f names55.txt > sequences55.sam