SAMMATE: input format to get transcripts quantities, alignment possibility

[behrooz darbani]

I am trying to use SAMMATE software that you have developed.
I am not a bioinformatician and just know how should work with Windows OS.

My question is about the file format that we should provide SAMMATE.

I have tried to use SAM files (produced by bowtie) both by aligning of reads to genome seq and transcript seq. I have annotations (GTF) in separate files (one fasta and one GTF annotations)! It is barley ref sequences recently produced.

However, when I try to analyze, SAMMATE indicates no reads aligned,....
It can read the GTF files and produce the excel files including the list of genes and their corresponding transcript isoforms but without any read count. All were zero.
when I analyze the same SAM files by other softwares I can get the quantities.

So, what should be the input file that I can use to get isoform specific quantities?
and, I have also tried to do the alignment by using SAMMATE, but I could not. Could that be due to the ref seq that I have in to separate files one with sequence (fasta) and another with annotations? what could be a solution?

Regards,
Behrooz

[Tin Chi Nguyen]

Hi Behrooz,

Currently SAMMate WinOS accepts both SAM and BAM files as inputs (not fasta files). If you are working with RNA-Seq data, you can align the reads against the reference genome using aligners that can align junction reads.You can also use bowie to align RNA-Seq reads but the junction reads will be missed. the output SAM/BAM file can serve as the input of SAMMate.

To be more clear, the procedure is as follows:
1/ Align fasta file against the reference genome
2/ Remember to set the unique alignment parameter (-g 1 if you are using tophat)
3/ Give the output BAM/SAM and the GTF file to SAMMate.
4/ Click on the Option button to open the option window. Select Iterative SASeq as the Transcript Abundance Estimator
5/ Click OK, press Run button. As the program runs, you can see the statistics about reads in the log panel (lower right)


If you have more question, just let us know. If you still have problem running it, I can try to debug if you send me your files


Best Regard,
Tin Nguyen

---

From: "behrooz darbani" <behrooz...@gmail.com>
To: asam...@googlegroups.com
Sent: Tuesday, February 5, 2013 5:19:48 PM
Subject: SAMMATE: input format to get transcripts quantities, alignment possibility

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