SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tool like FastQC ? patouch74 Bioinformatics 5 06-10-2014 07:10 AM
Query while using NGSQC Tool kit SubodhTambat RNA Sequencing 1 04-18-2014 01:22 AM
Query while using NGSQC Tool kit SubodhTambat General 0 04-18-2014 12:22 AM
poor quality on R1 end in SOLid fastqc test fankatt SOLiD 2 07-25-2013 02:18 AM
SOlid &&&& Metagenomics fanyucai1 Metagenomics 7 01-21-2013 10:08 PM

Reply
 
Thread Tools
Old 12-08-2014, 05:52 AM   #1
huma Asif
Member
 
Location: Japan

Join Date: Oct 2010
Posts: 53
Default SOLID & FastQC tool kit

Hello everyone,


I have SOLiD Mate pair data which I am trying to pass through QC checks. what i did so far
1) Convert XSQ to fastq (using XSQtools)
2)solid2fastq.pl from bwa
can i use this fastq files with Fastqc?
3)Quality assessment - Fastqc
2) Data cleaning - Quality trimming/ using FastX tool kit
can fastq_quality_trimmer handle this format?
3) Mapping using BWA(will do)

i will be extremely thankful If anyone else out there still uses SOLiD data and can give me some details of their workflows.

Regards
huma Asif is offline   Reply With Quote
Reply

Tags
bwa align color solid, fastq quality, solid 4, solid 5500, solid2fastq.pl

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 09:02 PM.


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