Samtools: Get Alignment (No Overlap)

Question

[Zhshqzyc]

If a chromosome region is given, which command can get the sequence alignment without overlapping?

Thanks.

Answer 1

[Zhidkov]

did you look on samtools FAQ? http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ

[Zhshqzyc]

I looked at it but there are many samtools command options. I still don't understand it. For ex, IF position is chr21:38781803-38782933, then what is the command?

Answer 2

[Sean Davis]

From the samtools help or the samtools website:

samtools view BAMFILE chr2:1,000,000-2,000,000

If this does not do what you want, perhaps you can clarify your question a bit.

[Zhshqzyc]

The output contains the raw data with overlap. But I don't want overlap.

[Zhidkov]

don't forget to put in new bam file, so you have to add > new.bam

[Sean Davis]

You will need to write code to get reads that do not overlap other reads. I do not know of a simple tool that pulls out only reads that do not overlap other reads.

[Zhshqzyc]

Socan we convert .bam to .fasta file? Then we can use microsoft biology tools get the result simply? Microsoft biology tools can open a fasta file and get the alignment sequence.

[Ketil]

If the bam file is sorted, this shouldn't be hard - just output the first read, and drop the reads starting before its end. But why would you want this?

[Zhshqzyc]

Okay. So you meant using samtools sort -o in.bam out.prefix? How can I get the first read? The bam file is to big, 200gb. How long it will take?

[Sean Davis]

"samtools view BAMFILE | head -1" will give you the first read. I think that Ketil and I still have no idea what you want to do, though. Please edit your original question with quite a bit more detail.

[Ketil]

zhshqzyc: why don't you extract a smaller data set and experiment a bit with samtools? If you have illumina reads, you could use 'head -40000 data.fq > small_data.fq' to extract the first 10K reads. That should be a bit more manageable than your 200G file and help you work out what you want to do, and how to achieve it.