Coverage calulation for each transcripts for variant analysis in RNA-seq data

Question

[mks002]

Hello everyone,

After performing variant analysis on RNA-seq data, i wanted to know coverage for each transcripts at 1X and 5X. I tried using GATK depth of coverage tool in Galaxy but it gave error. I also tried doing it using RSeQC. Nthg much is working out there. Using bedtools i can do but right now i dont have local server, so depended on using online server.

I wanted to know if some other tool or way is there calculate the coverage at 1X and 5X, since it would be helpful for me to find the full length transcripts observed.

Waiting for response , thank you in advance.

[WouterDeCoster]

calculate the coverage at 1X and 5X

What does that mean?

I tried using GATK depth of coverage tool in Galaxy but it gave error. I also tried doing it using RSeQC. Nthg much is working out there.

Without telling us what exactly went wrong we can't help you.

See also Brief Reminder On How To Ask A Good Question

[mks002]

Thank you for your reply.

Coverage at 1X means - At depth of 1X (at least one read) how much is the length of transcript we are covering, similarly at 5X.