A filtering program for filtering SOLiD reads directly without converting to fastq was described in http://bioinformatics.oxfordjournals.org/content/26/6/849.short?rss=1 and should have been available at http://hts.rutgers.edu/filter
Unfortunately, that website is closed. Would anyone have a copy of the program?
•
written
by
lin.barnum •
2 answers
Here is the Perl script: https://github.com/fls-bioinformatics-core/HTS_SOLiD_Preprocessing [moved from my old Dropbox folder 20 Oct. 2015]
We still use this script to prefilter SOLiD sequencing runs.
I wrote this: https://github.com/brentp/bio-playground/blob/master/solidstuff/solid-trimmer.py
which can trim a .csasta + .qual file and output the format of your choosing (BWA/BFAST or csfasta and qual)
If you're talking about their hdf5 formatted data, I don't know of a tool to trim directly from that without exporting first.
Log in to answer this question.
-
The difference between Copy Number Alterations, Copy Number Aberrations (CNAs) and Copy Number Vari…
written by Ward Weistra
-
Looking for a short read mapping tool (Bioinformatics) based on Hadoop YARN
written by benarnon •
-
Is There A Faster Replacement For Fastq-Dump (From The Sra-Toolkit)?
written by Devon Ryan
-
Solid Mate-Pair Alignment With Bwa
written by lin.barnum •
-
Best Practice Approach In R To Processing Illumina Microarrays For Rna Profiling
written by Brian Tsai •
-
Identity-By-Descent Used To Narrow Down Targets From Exome Sequencing Data
written by michealsmith
-
Can You Use Flapjack To Group Individuals Into Cultivars?
written by Philipp Bayer
-
Mapping Paired End Solid Data Using Bwa
written by Mahdi Sarmady
-
Java Parser For Bigwig ?
written by Pierre Lindenbaum
-
How To Get Swissprot Release 49?
written by Marcinmagnus •
Well there are many other scripts available that will do the same job. Some of them are even faster than what you are talking about. If I remember it correctly they wrote a perl code. Search for filtering SOLID reads in the forum and you will get many posts about it.