Counting reads on genome

Question

[EVR]

Hi,

I aligned my reads to de novo transcriptome using bowtie. Now the unaligned reads from the previous step was mapped to genome using tophat2. Now I would like to count the reads mapped to every scaffold and along the coverage region. How can I achieve this as tools like tophat,feature counts requires gtf file which has location of transcripts in every scaffold.But here the unaligned reads are mapped outside of the transcripts and hence I dont know whether using GTF file will be appropriate.

Any guidance wil be highly useful.

Thanks in advance

Answer 1

[mastal511]

Samtools idxstats should give you the number of reads mapped to every reference sequence in your genome file.

See the samtools manual:

http://www.htslib.org/doc/samtools.html

[GenoMax]

Qualimap also provides a nice visual summary for BAM files.

[EVR]

@mastal511 and @genomax2 Thanks for your guidance. I estimated the reads like you said. Now how can I get the coverage information i.e. in scaffold_XX the region between 23445 and 23670 contains 200 reads. Can I make use of genome coverage? Kindly guide me

[GenoMax]

What question are you trying to answer after this step (or in general)?