SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
How good bowtie can map SOLiD data? ypsd SOLiD 11 12-17-2012 08:56 AM
ABI-SOLID data with Bowtie-0.12.7 and TopHat-1.1.2 repinementer Bioinformatics 17 04-19-2011 09:10 AM
Bowtie Solexa data analysis help Ka123$ Bioinformatics 11 09-17-2010 12:37 AM
Bowtie & Samtools Questions with SOLiD data earisme Bioinformatics 1 09-16-2010 02:34 PM

Reply
 
Thread Tools
Old 10-11-2010, 09:20 PM   #1
wangleibio
Junior Member
 
Location: shanghai

Join Date: Nov 2009
Posts: 8
Default question about Solid data analysis using bowtie?


hello ,everyone
I am trying to run bowtie with the solid sequence data flower9_1_F3.csfasta and flower9_1_F3_QV.qual
I built the bowtie-build -C index successfully and moved the generated index files to the Bowtie indexes subdirectory. I run the command:
bowtie -n 3 --best --strata -a -e 150 -p 4 ../cDNA_reference/TAIR9_cdna -C -f flower9_1_F3.csfasta -Q flower9_1_F3_QV.qual --un fllower9-unmap > flower9-map &
and the output i got is an error showing on console

[wanglei@mu01 data]$ [wanglei@mu01 data]$ Too few quality values for read: 425_2031_2008_F3
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
Too few quality values for read: 425_2042_1847_F3
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
Too few quality values for read: 1277_2042_2013_F3
are you sure this is a FASTQ-int file?
Could you please help me to sort out this issue?
thanks
wanglei
wangleibio is offline   Reply With Quote
Old 10-12-2010, 12:36 AM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Please only post to one forum. Cross-posting is like spam, unacceptable.
nilshomer is offline   Reply With Quote
Old 10-12-2010, 03:38 AM   #3
wangleibio
Junior Member
 
Location: shanghai

Join Date: Nov 2009
Posts: 8
Default

ok,i have deleted it, thanks!
wangleibio is offline   Reply With Quote
Old 10-22-2010, 12:42 PM   #4
adamdeluca
Member
 
Location: Iowa City, IA

Join Date: Jul 2010
Posts: 95
Default Truncated Qual file

I have had this error when SAET failed and a truncated qual file was produced.
adamdeluca is offline   Reply With Quote
Old 10-20-2012, 01:18 PM   #5
Chirag
Member
 
Location: Norway

Join Date: Nov 2011
Posts: 23
Default

Hey guys,
How did you solve this problem ? Could you please help me with this ?
I am also getting this error, when using tophat mapping on colorspace file.

This is my command: [Works fine until half-way]

tophat --output-dir /results --color -p 8 --no-coverage-search /bowtie_alignment_reference/mm9_c F3.csfasta F3.QV.qual


I get this error:
Mapping left_kept_reads_seg1 to genome mm9_c with Bowtie (1/3)
Mapping left_kept_reads_seg2 to genome mm9_c with Bowtie (2/3)
Mapping left_kept_reads_seg3 to genome mm9_c with Bowtie (3/3)

[2012-10-20 22:11:02] Mapping right_kept_reads to genome mm9_c with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 39 I
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'


regards
Chirag
Chirag is offline   Reply With Quote
Old 03-26-2013, 07:32 AM   #6
Jetse
Member
 
Location: The netherlands

Join Date: Nov 2012
Posts: 38
Default

Did anyone of you solve this problem?
I have exactly the same problem now.

Mapping left_kept_reads to genome GRCh37_gatk_colorspace with Bowtie
Mapping left_kept_reads_seg1 to genome GRCh37_gatk_colorspace with Bowtie (1/2)
Mapping left_kept_reads_seg2 to genome GRCh37_gatk_colorspace with Bowtie (2/2)
Mapping right_kept_reads to genome GRCh37_gatk_colorspace with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 28 I
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'

All 4 files are exactly 200000 lines (so 100000 reads). Mapping the left reads works, but when mapping the right reads it fails...

[EDIT]
For anyone who has this error too, check whether you have added the --quals option, also check the command on order of files (first all csfasta files than the qual files). This solved my error...

Last edited by Jetse; 03-26-2013 at 09:02 AM. Reason: solved
Jetse 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 02:30 PM.


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