genome coverage by samtools

Question

[zizigolu]

Hey friends,

I have a bam file (also a bed file getting from bam to bed in galaxy), and a fasta.fai reference genome

I need genome coverage, I tried many ways, at last I found a post telling this command

samtools mpileup -ABQ0 -d10000000 -f ref.fas qry.bam > qry.mpileup

I'm on Windows

My reference genome name is sequence.fasta.fai

My bam file name is eg1.bam

and both files are placed in C:\Users\yang\Documents\Downloads\samtools

Now, which I should type in cmd instead of above command?

[Sean Davis]

I noticed that you have asked a number of questions on Biostars recently. Judging from some of those questions, I would suggest that you work with your advisor to develop a plan to get you the training you need to be successful in a time-frame that is acceptable to both of you. Biostars is a great place to come for answers to questions, but it seems that you would benefit from some baseline training before trying to embark on some of these analyses yourself. My comments are not meant to discourage you from asking questions here, but more directed to helping you be successful.

[zizigolu]

You are right but believe that, right now, asking questions here is my only way to get my answers.

[Sean Davis]

It may feel that way, but there are online courses, youtube videos, tutorials, books, and some packages have extensive documentation. There is also training available at courses and even at some international meetings. Collaborators are available, also. If you are in Berlin (it seems so), potential collaborators may be local. If not, skype works great.

[Sean Davis]

See Bioinformatics online course for some online course examples.

[zizigolu]

Thank you

Answer 1

[Sean Davis]

The reference genome that you are using is sequence.fasta, not sequence.fasta.fai. The latter is an index to the reference sequence and not the reference sequence itself. Replace ref.fas with sequence.fasta and qry.bam with eg1.bam and that should do it.