SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
.abi to fasta/fastq conversion script/program? AppleInformatics General 12 08-26-2012 11:17 PM
Perl script to convert BAM to BED? rebrendi Bioinformatics 3 03-22-2012 11:34 PM
Script to convert 75x35 bp to 50x35 bp reads SOLiD 5500 paolo.kunder SOLiD 1 11-30-2011 07:27 AM
Convert FASTA to FASTAQ jomaco Bioinformatics 6 10-31-2011 11:14 AM
Script to remove gap-only sites from fasta alignment? kmkocot Bioinformatics 4 02-23-2010 10:50 AM

Reply
 
Thread Tools
Old 01-26-2012, 11:21 PM   #1
Lizex
Member
 
Location: Cape Town South Africa

Join Date: Feb 2011
Posts: 22
Default Bioperl Script to convert fasta to fq

Hi pkerrwall your answer to this question:

The problem with this script is that it returns the reference DNA sequence (from the genome fasta file used for mapping) for the transcripts and not the assembly from the mapped reads.

Does anyone know of a tool that can give the assembled transcript sequence from the RNA-seq data? Or can someone help me if I'm misunderstanding GFFRead?

Here is the process that I am using:

samtools mpileup -uf ref.fa accepted_hits.bam | bcftools view -cg - | vcfutils.pl vcf2fq | fq2fa.pl > new_ref.fa
gffread -w transcripts.fa -g new_ref.fa transcripts.gtf

where fq2fa.pl is a bioperl script to convert from fq to fasta

I also have an email into the cufflinks developers to see if there is a way that the gffread utility can be enhanced to get the consensus sequence from the bam file and not the reference genome.

Could you make the bioperl script: fq2fa.pl and vcfutils.pl and vcf2fq available.

Lizex
Lizex is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:49 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO