SOLiD paired-end mapping

[yaira04]

Hi all,
until recently I mapped my SOLiD single-end reads using Bowtie aligner.
Now, I'm trying to map a SOLiD paired-end reads (not mate-paired) and struggling some difficulties....
Does anyone know a way to map paired-end reads?
Thanks!

[nilshomer]

You can use novoalign, bwa, bfast+bwa, or shrimp2.

[yaira04]

Thanks nilshomer!

Does BWA fits paired-end data??
I read that one should reverse and complement the reads before using BWA aligner for that data. Is it true, and if so how should it be done?

[yaira04]

Thanks nilshomer!

Does BWA fits paired-end data??
I read that one should reverse and complement the reads before using BWA aligner for that data. Is it true, and if so how should it be done?

[nilshomer]

It should be too hard to test out the behavior yourself by making up some fake reads etc. Otherwise, a new post may be in order.

[pishotta]

If you're trying to use bowtie...

FYI: Not crazy about bowtie alignment for my SOLiD 5500XL paired-end, color-space, direct-from-XSQ files, but a command of the following form works:

bowtie -p 4 -C -S BT_CS_Index_hg19 --fr -f -1 F3end_1.csfasta -2 F5end_2.csfasta --Q1 F3end_1.QV.qual --Q2 F5end_2.QV.qual output.sam

Note the "--fr". That is not the default.

Gets only about a third of the reads. Lifescope aligner w/ SAET (proprietary) works best, but SHRiMP pretty good. Still evaluating.

-- Fred P.

[carmeyeii]

Hi!

I'm analyzing a "second-hand" dataset generated using SOLiD 4. It is a transcriptome mate pair library that is 52 x 37 nt, and I cannot for the sake of me find the protocol that was used to generate those specific read lengths. I have F3 and R3 reads, so I am assuming it is a circularization protocol, but I do not know what the size selection parameters were, or how the circles were cut to produce the final fragments. This info would be very valuable for a more accurate mapping.

Any knowledge would be greatly appreciated!

Thanks a lot,

Carmen