Question: Counting reads on genome
0
gravatar for EVR
3.7 years ago by
EVR570
Earth
EVR570 wrote:

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

transcriptome rna-seq genome • 1.1k views
ADD COMMENTlink modified 3.7 years ago by mastal5112.0k • written 3.7 years ago by EVR570
0
gravatar for mastal511
3.7 years ago by
mastal5112.0k
mastal5112.0k wrote:

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

ADD COMMENTlink written 3.7 years ago by mastal5112.0k

Qualimap also provides a nice visual summary for BAM files.

ADD REPLYlink written 3.7 years ago by genomax75k

@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

ADD REPLYlink written 3.7 years ago by EVR570

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

ADD REPLYlink written 3.7 years ago by genomax75k
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