SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
tophat seq length qual length mismatch error epi Bioinformatics 3 09-10-2012 01:43 AM
picard error: Mismatch between read length and quals length writing read shawpa Bioinformatics 0 08-20-2012 05:52 AM
qual length error when run tophat HSV-1 RNA Sequencing 1 08-12-2012 02:54 PM
beginning of quality values record not found & qual length () differs from seq length papori Bioinformatics 1 07-09-2012 12:25 PM
samtools view error: CIGAR and sequence length are inconsistent (tophat/bowtie) glacierbird Bioinformatics 2 06-29-2010 01:58 AM

Reply
 
Thread Tools
Old 01-15-2013, 10:30 AM   #1
JenBarb
Member
 
Location: Bethesda, MD

Join Date: Oct 2010
Posts: 47
Default Tophat error: Error: qual length (113) differs from seq length (101) for fastq record

I am getting a couple of errors like this on two out of 18 of my files. Has anyone seen this and if so, does anyone know what it means or how to fix it?

Thanks,
Jen
JenBarb is offline   Reply With Quote
Old 10-20-2016, 09:07 AM   #2
ronaldrcutler
Member
 
Location: Virginia

Join Date: May 2016
Posts: 80
Default

As suggested by GenoMax, try this command to examine the offending record by pulling it out of the file
Code:
$ cat (or zcat) <fastq_file_name> | grep <sequence_identifier> -A 3
ronaldrcutler 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 11:15 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO