srf2fastq statistics

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srf2fastq specifications

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Unique identifier OMICS_05131
Name srf2fastq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SRF
Output format FASTQ
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL http://manpages.ubuntu.com/manpages.gz/trusty/man1/srf2fastq.1.gz
Maintained Yes

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srf2fastq citations

 (2)
library_books

A Gene Module Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer

2017
Comput Struct Biotechnol J
PMCID: 5683705
PMID: 29158875
DOI: 10.1016/j.csbj.2017.09.003

[…] somatic mutations were detected using the MuTect algorithm . The RNA sequencing data was generated from 539 tumor and 72 matched normal tissue samples. After poor quality reads were removed using the srf2fastq tool (Staden package), the RNA sequencing reads were aligned to reference transcript database using BWA algorithm . The genes that have the mean Fragments Per Kilobase of transcript per Mill […]

library_books

Fish the ChIPs: a pipeline for automated genomic annotation of ChIP Seq data

2011
Biol Direct
PMCID: 3201895
PMID: 21978789
DOI: 10.1186/1745-6150-6-51

[…] After conversion of either srf or sra raw files to fastq (using srf2fastq - a tool part of the Staden package [] - in case of srf or the SRA Toolkit [] in case of sra), quality control reports are generated using FastQC []. Reads are then aligned to a reference ge […]


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srf2fastq institution(s)
Wellcome Trust Sanger Institute, Hinxton, UK

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