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Old 02-01-2017, 04:51 AM   #3
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Location: Chile

Join Date: Feb 2014
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Originally Posted by Brian Bushnell View Post
No surprise there; the Solid platform had terrible quality, which is why it is now extinct.

Can you describe what you are trying to do, and why you are using Solid data to do it? I highly recommend not using Solid. In most cases, I think it's much more cost effective to sequence on Illumina and throw away Solid data, than analyze Solid data.
Hi Brian. I agree. Honestly, I think that color space Solid is not a very good option. In fact, are not there many softwares to deal with it, and the options to conversion to fastq (base space), are not too reliable.

Well, I'm trying to disclosing variants (SNPs and Indels VCF) in a human exome, associated to cancer. So, my pipeline to do this is:

Map to reference (Bowtie) --> Sam to Bam - statistics (Samtools - Picard) --> Post-alignment processing ( Remove duplicates - InDel realignment -  Base quality score recalibration) using Picard and GATK --> Variant calling (GATK) --> Annotate variants (ANNOVAR ?)
The problem is that to do this, the quality of mapping is necessary. But, the SAM file obtained after mapping with Bowtie, lacks all alignment fields like MAPQ or QNAME. So, I wonder if using color fasta-space and QV as input in Bowtie would not allow getting these fields like MAPQ (I have no experience with Solid), or maybe I'm doing something wrong.

This data was given to me, and I do not have the opportunity to sequence again using another platform like Illumina (if I could, I would do it without thinking).
Thank you for your response, and any suggestions will be welcome.


Last edited by Alexis1; 02-01-2017 at 05:38 AM.
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