Looking for the sequence of a particular transcript from sequencing data

the_august · 01-21-2019, 11:23 AM

First, let me tell you that I'm very new to the field of NGS and not much familiar with the set of tools commonly used for NGS data processing. However, I'm not new to Bioinformatics, and have quite some experience in Linux, Python, Perl , R etc.

I've to find out the sequence of a particular transcript from a set of mouse fastq files. I've extracted the sequence reads for this particular sequence using bbduk.sh of the bbmap package using the following command:

Code:

bbduk.sh  in=/me/clumpedSRA.fq.gz ref=/me/known_transcript.fasta k=13 outm=/me/knownT_reads_only.fastq

Can somebody tell me how to get the sequence of the transcript from this reads of the sequence of interest? Can any other tools from 'bbmap' be used?

Besides, I've access to Tophat and Trinity on a high performance cluster.

Thanks in advance

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
How to extract assembled transcript sequence from RNA-seq data instead of ref genome?	lzu	Bioinformatics	10	02-24-2014 01:56 AM
extra sequence following transcript in RNA-seq ?	FLYINGDOLPHIN	RNA Sequencing	5	11-14-2013 12:12 PM
Gene sequence from transcript sequence	Phantom123	Bioinformatics	0	07-19-2012 09:07 AM
Why do I find the sequencing primer sequence in my data?	soev	Bioinformatics	2	11-17-2011 03:07 AM
How to trim the adaptor sequence from the solexa small RNA sequencing data?	satp	Bioinformatics	11	11-17-2010 02:08 PM

01-21-2019, 11:23 AM	#1
the_august Junior Member Location: US Join Date: Jan 2013 Posts: 6	Looking for the sequence of a particular transcript from sequencing data First, let me tell you that I'm very new to the field of NGS and not much familiar with the set of tools commonly used for NGS data processing. However, I'm not new to Bioinformatics, and have quite some experience in Linux, Python, Perl , R etc. I've to find out the sequence of a particular transcript from a set of mouse fastq files. I've extracted the sequence reads for this particular sequence using bbduk.sh of the bbmap package using the following command: Code: bbduk.sh in=/me/clumpedSRA.fq.gz ref=/me/known_transcript.fasta k=13 outm=/me/knownT_reads_only.fastq Can somebody tell me how to get the sequence of the transcript from this reads of the sequence of interest? Can any other tools from 'bbmap' be used? Besides, I've access to Tophat and Trinity on a high performance cluster. Thanks in advance