bioscope single read BAM & Cufflinks

[tdm]

Dear Adam,
I would like to know to what extend is the compatibility with bioscope bam files ?
I produce BAM files with the single read pipeline, but Cufflinks still bother me with XS attribute.

It work if i add this specific column with the awk command found in this forum :

awk -F'\t' 'BEGIN { OFS="\t"} {if($2==16) {$(NF+1)="XS:A:-"; print $0,$(NF+1)} else {$(NF+1)="XS:A:+"; print $0,$(NF+1)}}' test.sam > test.sam2

Thx for the support you provide in these forums
Thibault

[adarob]

Proper support for SOLiD reads will be added to Cufflinks in the next couple of days. You will not need to alter the SAM file, but will simply use the option --library-type fr-secondstrand. I apologize for the slight delay in this new version, but we are trying to get a couple of other bug fixes in.

In the meantime, the command you mention should accomplish the same thing, but will not work for paired-end reads.

-Adam

[rainer]

Tried Cufflinks 0.9.3 with AB Bioscope 1.3 generated BAM file (SOLID 50x25 paired end reads).
I used the --library-type fr-secondstrand parameter for the SOLID data.

Yet, Cufflinks seems to determine the read length wrong:
"Read Type: 25bp paired-end" instead of 50 x 25

Re-tried it with 50 bp fragment data -> Cufflinks determines 25 bp

Rainer

[tdm]

I have the same message, cufflinks 092 and bioscope 1.2
Maybe it is just a typing error with the message about read type.

[rainer]

Maybe it is just a typing error with the message about read type.

I don't think that it comes from the read type. Same thing if you use other options for read type.

Rainer

[tdm]

From source code, its the minimum read length. There is also a maximum, but not displayed. I think it is alright.

[adarob]

Yes, tdm is correct. It was not set up for mixed read-lengths, but I will be changing (or removing) this message soon.