Hello,
I have a pretty basic question. I hope to get help in this matter.
We did this whole genome targeted sequencing earlier. Now we need only a partial chr1 sequence aligned with the reference genome, instead of doing the alignment and mapping all over again.
I took chr1 of the ref genome as a complete reference and alignment the mate pair fastq files. but I am stuck at this point again. Can anyon help.
Its chicken genome.
Aini
Do you want to align only 1 chr1 sequence to the reference genome? Is that your question ?
yes, infact, I have a specific location to align that is associated with my trait of interest e.g. 1:67,246,039- 67,350,164. And I have raw mate pair fastq files.
I have created a bam file using bowtie2. Ref file is chr1 of the reference genome. with 2 mate pair fastq files.
here is the same result:
But i cannot extract the coordinates as you suggested: Antonio R. Franco
I dont understand, what to do at this point
You are doing right in reding these instructions http://www.htslib.org/doc/samtools.html. samttools view had some requirements, like the presence of the header. If you want, share your bam file with me through dropbox, mega or the like, and I give it a look. My address is arfranco (@) uco.es