trans abyss assembly

[papori]

hey all, i am using trans abyss for de novo assembly.
When i am running the assembly level for k=26(example) i am getting this kind of output:

>11 3814 208317 9+,0+,5-,0+,5-,0+,5-,0+,5-,0+,2+
CTTGGTGAATTGGCTCCCGAAGCTCCTGCTGCTTGGAGTGGGTGACCT......

can anyone explain me What does the numbers in the " > " line means?


thanks in advance...

[burt]

Hey, I've been playing around with trans-abyss for RNA-seq data. Erm, what mode/stage of trans-abyss did you ran? I don't seem to remember coming across those kind of output for trans-abyss.

In fact trans-abyss has a specific output folder for each stage of the pipeline. This is described in the flow diagram of the trans-abyss pipeline in their paper.

[papori]

thanks mate, i got the answer already in trans abyss group..

For this line:

>11 3814 208317 9+,0+,5-,0+,5-,0+,5-,0+,5-,0+,2+
It means this contig ID is 11, its length is 3814, its kmer coverage is 208317, and the final string "9+,0+,5-,0+,5-,0+,5-,0+,5-,0+,2+" is the path of contig nodes that made up this contig.
Rong

[blindtiger454]

it's a little off subject, but I've been curious about using trans abyss. How does the program output transcript variants of the same gene? Newbler uses the isogroup & isotig style, and I've heard velvet/oases uses a similar description. Can trans abyss do the same thing, labeling at the transcript and gene level?