SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD



Similar Threads
Thread Thread Starter Forum Replies Last Post
question about Solid data analysis using bowtie? wangleibio RNA Sequencing 5 03-26-2013 06:32 AM
How good bowtie can map SOLiD data? ypsd SOLiD 11 12-17-2012 07:56 AM
ABI-SOLID data with Bowtie-0.12.7 and TopHat-1.1.2 repinementer Bioinformatics 17 04-19-2011 08:10 AM
Bowtie & Samtools Questions with SOLiD data earisme Bioinformatics 1 09-16-2010 01:34 PM

Reply
 
Thread Tools
Old 05-05-2012, 05:39 AM   #1
kentsing
Junior Member
 
Location: Guangzhou China

Join Date: May 2012
Posts: 1
Default How can i use bowtie to map solid data

Dear Sir or Madam:
i am a fresh man to solid data and bowtie.
I try to aln my reads file to human genome wiith command:

"/data1/tools/bowtie-0.12.7/bowtie -q -p 6 -l 27 -n 2 -m 3 -e 950 -k 1 -S /data5/project/luo/index/Human_Genome SRR121550.fastq SRR121550.sam"

and get the following error message:
#################
Reads file contained a pattern with more than 1024 quality values.
Please truncate reads and quality values and and re-run Bowtie
##################

then i checked my fastq file and i found the fastq file contain the reads info like this

:@SRR121551.5 r1ahead05_20090410_1_cd4_5_8_1_32_149 length=35
T32222220222201131111312222111131212
+SRR121551.5 r1ahead05_20090410_1_cd4_5_8_1_32_149 length=35
!7;/&##%'&'#$''&$&/'-)-%#$#*&$1$%#%.

it's seems not a valid fastq file , but why??


I use the followling command to dump sra to fastq

/data1/tools/sratoolkit.2.1.9-centos_linux64/fastq-dump /data6/nuclesome/SRR155510.sra

pls help ! thx!!!
kentsing is offline   Reply With Quote
Old 05-23-2012, 08:05 AM   #2
bsuac6
Junior Member
 
Location: UK

Join Date: Sep 2010
Posts: 9
Default

The bowtie command needs -C, as it is color space. Which is also why your reads are like this: T32222220222201131111312222111131212

Not sure if there are any other problems with your fastq file but I would try adding -C to the bowtie command and see if it works.
bsuac6 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 09:59 AM.


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