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SOLiD WT Analysis pipeline Alignment
Hello all,
I'm using the SOLiD WT pipeline ver 1.2.1 (also called "Pre-Bioscope") to map a 50 bp fragment library.
My results look good so far, but I don't understand the alignment process completely.:
The software splits the reads in 2 anchors. Each anchor can have 2 mismatches by default. Are these 2 missmatches in colorspace or basespace? Also, if I have one mismatch in colorspace (= one ligation reaction is wrong), can the software still guess the correct base sequence at that position by the surrounding color information?
Is it therefor more stringent to allow 2 mismatches in colorspace or 2 mismatches in basespace?
Also: After the anchors are aligned, they are joined. The program then uses a exon reference file to adjust the score of the read depending on the splice junction.
Does the software also use the exon reference file to map directly against junctions (known and putative) as it states in the documentation? If so, then why does is do the anchoring in the first place?
Best,
Seb
I'm using the SOLiD WT pipeline ver 1.2.1 (also called "Pre-Bioscope") to map a 50 bp fragment library.
My results look good so far, but I don't understand the alignment process completely.:
The software splits the reads in 2 anchors. Each anchor can have 2 mismatches by default. Are these 2 missmatches in colorspace or basespace? Also, if I have one mismatch in colorspace (= one ligation reaction is wrong), can the software still guess the correct base sequence at that position by the surrounding color information?
Is it therefor more stringent to allow 2 mismatches in colorspace or 2 mismatches in basespace?
Also: After the anchors are aligned, they are joined. The program then uses a exon reference file to adjust the score of the read depending on the splice junction.
Does the software also use the exon reference file to map directly against junctions (known and putative) as it states in the documentation? If so, then why does is do the anchoring in the first place?
Best,
Seb