what to do with this

[Kelly Lynn]

Hello,everyone. I'm suing: 'samtools view -c file.sorted.map chr1' to count the reads from the region "chr", but 'region"chr1" specifies an unknown reference name. Continue anyway.' is all I got. Anything wrong with the language or something else?

[westerman]

What are your reference names? You obviously believe that 'chr1' is one of your reference names but maybe it is not? For example in one of the BAM files I have handy, the references are called 'Group2', etc. so I can do:

samtools view -c wt.sr.bam Group2

But if I do a

samtools view -c wt.sr.bam chr1

Then I get the error you described.

In order to see your reference name I suggest doing a:

samtools view file.sorted.map | more

[Kelly Lynn]

thanks a lot westerman, the "chr1" is not my reference file, I guess the "chr1" string for hg19 refseq is enough for the region option? Should the 'region' be specified with the exactly same name as in the refseq, such like '>chr1_1:+' ? Or should I first pool the reference info into the memory then delivery them to the samtools view command, like:
cat reference.fa|samtools view myfile.sorted.bam chr1?
I tried in many ways, but still can not make this out.

[oiiio]

Kelly Lynn,

Sorry if this is an overly obvious question, but are you using a .bam or .sam file when you mention "file.sorted.map"? And if you are specifying a chromosome, then you must be using an indexed .BAM file.

Supposing you are using something like file.sorted.bam (with the index file.sorted.bam.bai in the same directory), maybe you could try this for your command line:

samtools view -c file.sorted.bam chr1

The term chr1 will work if that is indeed the name of the chromosome you are investigating. I just tried out the above command myself, and it worked fast and accurately.

[westerman]

thanks a lot westerman, the "chr1" is not my reference file, I guess the "chr1" string for hg19 refseq is enough for the region option? Should the 'region' be specified with the exactly same name as in the refseq, such like '>chr1_1:+' ? Or should I first pool the reference info into the memory then delivery them to the samtools view command, like:
cat reference.fa|samtools view myfile.sorted.bam chr1?
I tried in many ways, but still can not make this out.

Please try my last suggestion:

samtools view file.sorted.map | more

And paste into this thread the the first two output lines that contain reads. From my, admitted small, experience with hg19 your reference should be in the form 'chr1'. But we need to be sure. So pasting in those lines will give us a clue.