SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
For MAQ: Is there a Tool to convert sanger-format fastq file to illumina-fotmat fastq byb121 Bioinformatics 6 12-20-2013 02:26 AM
Ideas on collecting quality scores per base in an illumina fastq file brachysclereid Bioinformatics 11 12-05-2011 02:00 PM
Restriction digest of RNA /DNA hybrid Gillow Sample Prep / Library Generation 1 07-09-2010 06:27 AM
Reduce file size after Illumina FASTQ to Sanger FASTQ conversion? jjw14 Illumina/Solexa 2 06-01-2010 05:35 PM
In silico data sets from BACs for GAII Illumina CG&R Bioinformatics 1 12-16-2009 07:37 AM

Reply
 
Thread Tools
Old 03-17-2011, 09:07 AM   #1
berthold
Junior Member
 
Location: Central Europe

Join Date: Mar 2011
Posts: 5
Default in silico restriction digest of Illumina reads (fastq file)

Hi

I wonder whether anyone has a solution for a restriction digestion script that works on fastq files (Illumina reads), splitting any reads that contain the restriction site into two separate reads (and writing it back into the fastq file)?

Actually I am not so much interested in restriction as such - I have reads from co-ligated and nebulized PCR fragments, so I'd like to separate those reads at the ligation junctions, and I thought I could tweak a restriction script (preferentially, Perl) into doing that.

Any hints appreciated.

regards,
Berthold
berthold is offline   Reply With Quote
Old 05-13-2018, 07:57 PM   #2
gholmes
Junior Member
 
Location: Melbourne

Join Date: May 2016
Posts: 1
Default

Hi Berthold,

Did you ever find a solution to doing in silico digestion of fastq files and writing output back into fastq format files? I've been trying to do this with the Bio.Restriction module of BioPython, but the output is fasta (with read quality data being lost).

Regards,
Gareth
gholmes is offline   Reply With Quote
Old 05-14-2018, 12:54 AM   #3
berthold
Junior Member
 
Location: Central Europe

Join Date: Mar 2011
Posts: 5
Default

Thanks for the hint Gareth.
No I did not find a way to do it otherwise yet (but it wasn't high priority). There's a student in my group now who is good with Python, I'll consult with him.

best regards,
Berthold
berthold is offline   Reply With Quote
Reply

Tags
fastq, illumina, pcr, perl, restriction enzyme

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 11:16 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO