SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Merging paired end reads for BLAST JJenks Bioinformatics 9 11-05-2018 10:40 AM
A question on Illumina paired-end reads alignment. Merging from different samples linudz Bioinformatics 4 02-27-2017 11:16 AM
Merging non-overlapping paired end reads karenr Illumina/Solexa 9 12-16-2016 07:02 PM
Merging illumina V4 paired end reads rEDI Illumina/Solexa 8 09-09-2016 09:10 AM
Merging paired end reads (R1 and R2 files) vectorborne5 Illumina/Solexa 2 10-09-2013 11:13 AM

Reply
 
Thread Tools
Old 03-07-2019, 03:54 PM   #1
rexxi
Member
 
Location: Santiago, Chile

Join Date: Jun 2012
Posts: 20
Talking Is there a paired end joiner which writes also the reads before merging?

Hi, I have a weird question. But I'm looking for a software which not just merge the paired reads but also writes them in a new file.

When a software matches a pair of reads it writes them in the output fastq (or fasta), but you don't have the option of knowing what they paired. I've checked some of them but mostly they create a file with the unpaired reads as the set of the discarded ones. I've been trying to find one which would give an output like that

SAMPLE_MATCHED_FORWARD.fastq
SAMPLE_MATCHED_REVERSE.fastq
SAMPLE_JOINED.fastq

the first two files would contain the reads that are going to be merged, but have been already found their mate. Is there a software with an option like that? I know it sounds weird but it could help me to discriminate from a pool containing a lot of unwanted sequences from different sources.

thanks for your time.
rexxi is offline   Reply With Quote
Old 03-11-2019, 02:46 PM   #2
torben
Member
 
Location: Norway

Join Date: Oct 2012
Posts: 19
Default

If it's not a problem to run the command twice, bbmerge can do this:

Code:
bbmerge.sh in1=SAMPLE_INPUT_FORWARD.fastq in2=SAMPLE_INPUT_REVERSE.fastq
out1=SAMPLE_MATCHED_FORWARD.fastq out2=SAMPLE_MATCHED_REVERSE.fastq merge=f
Code:
bbmerge.sh in1=SAMPLE_INPUT_FORWARD.fastq in2=SAMPLE_INPUT_REVERSE.fastq
out=SAMPLE_JOINED.fastq merge=t
Run bbmerge.sh without options for a list of possible options. See also this thread.
torben is offline   Reply With Quote
Reply

Tags
illumina, match reads, paired end

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 11:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO