Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Sanger sequencing - How to get consensus sequence from forward and reverse strand? treeofpeace Bioinformatics 1 04-17-2018 11:07 AM
Exome sequencing quality filtering Kath Bioinformatics 1 07-20-2013 06:58 AM
filtering strategy in exome sequencing and quality control Groningen Bioinformatics 1 03-12-2013 12:40 PM
Sanger FASTQ Quality Scores upper Bioinformatics 2 05-03-2010 07:20 PM
New merge function creates Sanger Quality Sequence from NGS paired end reads SoftGenetics Vendor Forum 0 02-23-2010 07:29 AM

Thread Tools
Old 05-03-2018, 12:02 AM   #1
Junior Member
Location: Germany

Join Date: May 2018
Posts: 1
Exclamation filtering out low quality sequences from Sanger Sequencing

I am currently facing a challenge of filtering out low quality sequences (output from Sanger sequecing, and roughly I have 300 sequences to process).

Below, I explain what I have done so far, any hints/tips to get this working are very much appreciated.

1- conversion ab1 to fastq "for filename in *.ab1; do seqret $filename fastq_files/$filename.fastq -osformat fastq; done"

2- trimming sequencing "for filename in *.fastq; do fastx_trimmer -f 30 -l 600 -i $filename -o t_$filename ; done"

3- trying to filter the sequences using " quality fastq_quality_filter -i input.fastq -o output/output.fastq -q 20 -v -Q 33 " and I got the following error message,

*** stack smashing detected ***: fastq_quality_filter terminated
zsh: abort (core dumped) fastq_quality_filter -i PosKonR.fastq -o output/Pos.fastq -q 20 -v -Q 33

I changed to -Q 64 and got " fastq_quality_filter: Invalid quality score value (char '&' ord 38 quality value -26) on line 4 "

Many thanks in advance for any help how overcome this issue.
MAmineHassani is offline   Reply With Quote
Old 05-03-2018, 03:47 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978

GenoMax is offline   Reply With Quote

filtering reads, sanger sequence analysis

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 04:23 AM.

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