Chip-Seq Txt Data Into Sam Format.

Question

[Kasthuri]

Hi:

I am a newbie here trying to convert the following chip-seq data given in txt format to a SAM format. Any thoughts on how to do this? Thanks.

chrom index forward reverse
chr01 146 0.0 1.0
chr01 254 0.0 3.0
chr01 319 0.0 1.0
chr01 328 0.0 1.0
...

[Neilfws]

Would be useful to know (1) to what index, forward and reverse refer and (2) what the desired SAM format looks like.

[Michael]

This is not possible, you must align your reads if you want sam format!

[Michael]

Your txt format looks like a list of peaks, is it that? Tell me what you are trying to do and which software you are using, then maybe we can help better. I guess, there must be something odd with the approach in general, when you want to go back one step from peaks to alignments.

[Mikael Huss]

This looks like GeneTrack data. http://atlas.bx.psu.edu/genetrack/docs/genetrack.html

Answer 1

[Michael]

There have been several questions already on converting <some format> to SAM. It is important to understand that you cannot simply convert any format, because the information contained must be similar for a conversion to make sense. SAM is a format for the result of short reads (pairwise) aligned against a reference sequence. In the strict sense of your question: the conversion you are looking for does not exist.

You can get SAM format anyway: Align your chipseq reads (in fasta or fastq format) against the reference genome using an aligner that outputs SAM format, there you go.

Look at the Box "Related" on the right to find the answers to similar problems ->

[Kasthuri]

Thank you Michael. I was thinking about this too. I understand that SAM is for alignment and converting the text to FASTA makes more sense than to SAM. However, I am working with two programs in which one needs SAM and the other, the txt format. I really don't think I have to align in order to compare these two and hence the question. Thanks a bunch, anyway. It validates my understanding. May be txt->FASTA->SAM may be the right way to go.

[Michael]

Your txt format looks like a list of peaks, is it that? Tell me what you are trying to do and which software you are using, then maybe we can help better.