How many reads by contigs with Ray ?

Question

[prpadi]

Hi all,

I have assembled a transcriptome using Ray. How can I have the numbers of reads by contig ?

I took the reads used to generate the assembly and aligned them to the assembled contigs using BWA to get the unmapped reads, which are the non-assembled reads (singletons). So I have a SAM format output. Maybe can I use samtools to get the reads number by contigs ?

Thank you for your help.

[prpadi]

Ok,

And it's not possible to have the number of reads by contigs directly with Ray ?

[Devon Ryan]

No clue, never used it. The grep ... command that I gave will be quick enough.

Answer 1

[Devon Ryan]

If you sort and index the BAM file, then you can just use samtools idxstats. Alternatively, samtools view foo.bam | cut -f 3 | sort | uniq -c will work on unindexed and unsorted files. For a SAM file, that last command could be simplified to grep -v "^@" foo.sam | cut -f 3 | sort | uniq -c.

Answer 2

[namratapatel183]

How can i get which reads were used in each contig in Ray afg file.

I tried to extract read information from the .afg file but it gives numbers instead of Read Ids, what this numbers represent in ray afg file?

Thank you for your help.

[h.mon]

Please open a new question instead of asking on another question.