Dear all,
been trying to explore a number of Helicos runs. I have access to the read data both in Helicos' SMS format as well as their implementation of SRF (which does not bode well). Using the Staden iolib package it is straightforward to convert reads to FASTA using the srf2fasta command:
Trying the same with srf2fastq results in:
My guess is that the quality information is encoded differently in the Helicos' implementation which would explain why Helisphere also only ships with a '2fasta' option.
Is there *any* way to get FASTQ (or a equivalent expressive format) out of Helicos? I'd love to throw the data at a few standard pipelines that usually start with FASTQ data, and seem to be out of options.
Thanks!
been trying to explore a number of Helicos runs. I have access to the read data both in Helicos' SMS format as well as their implementation of SRF (which does not bode well). Using the Staden iolib package it is straightforward to convert reads to FASTA using the srf2fasta command:
>HE-0243693211002-14-2-2-4250
CAGAGTATAGACCTA
CAGAGTATAGACCTA
Zero or greater than one CNF chunks found.
Is there *any* way to get FASTQ (or a equivalent expressive format) out of Helicos? I'd love to throw the data at a few standard pipelines that usually start with FASTQ data, and seem to be out of options.
Thanks!
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