Question: genome coverage by samtools
0
gravatar for A
4.9 years ago by
A3.7k
A3.7k wrote:

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

im in window

my refence genome name is= sequence.fasta.fai

my bam file name is= eg1.bam

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

now, which i should type in cmd instead of above command???

ADD COMMENTlink modified 4.9 years ago by Sean Davis26k • written 4.9 years ago by A3.7k
3

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 timeframe 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.  

ADD REPLYlink written 4.9 years ago by Sean Davis26k

you all right...but believe that, right now, asking question here is my only way to get my answers...

ADD REPLYlink written 4.9 years ago by A3.7k
1

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.  

ADD REPLYlink written 4.9 years ago by Sean Davis26k
1

See Bioinformatics online course for some online course examples.

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by Sean Davis26k

thank you

ADD REPLYlink written 4.9 years ago by A3.7k
0
gravatar for Sean Davis
4.9 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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.

ADD COMMENTlink written 4.9 years ago by Sean Davis26k
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