Question: How many reads by contigs with Ray ?
0
gravatar for prpadi
5.0 years ago by
prpadi10
Germany
prpadi10 wrote:

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, wich 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.

rna-seq next-gen assembly • 1.3k views
ADD COMMENTlink modified 4.0 years ago by namratapatel18310 • written 5.0 years ago by prpadi10

Ok,

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

ADD REPLYlink written 5.0 years ago by prpadi10

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

ADD REPLYlink written 5.0 years ago by Devon Ryan90k
0
gravatar for Devon Ryan
5.0 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

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.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Devon Ryan90k
0
gravatar for namratapatel183
4.0 years ago by
namratapatel18310 wrote:

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.

ADD COMMENTlink written 4.0 years ago by namratapatel18310

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

ADD REPLYlink written 4.0 years ago by h.mon25k
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