Error using tophat mapping AB SOLiD color space data

[Luyi Tian]

I got an error when I try to use tophat analysing Solid data from:

http://www.ncbi.nlm.nih.gov/sra/?term=SRR545797

and the err report is:

[2012-09-11 00:43:09] Mapping left_kept_reads to transcriptome M_genes with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 32T3@
are you sure this is a FASTQ-int file?
Command: /usr/local/bin/bowtie -q -C --col-keepends -v 1 -k 60 -m 60 -S -p 4 --sam-nohead --max /dev/null M_heart2_9out/tmp/M_genes -

but I don't understand the read-name '32T3@'. the format of my fastq is like this:

@SRR545797.117 1_35_540 length=50
T10223131112013200331001120211030313103322000132033
+SRR545797.117 1_35_540 length=50
!@@@8@@@@@?@@@@@@@;@@@@@@@2?-/-@6//6/5=@2?@6./2@28.

So I tracked down the source code of bowtie and rewrite and rebuild the err report function so that it could also report the sequence and quality scores. Then my err report turned to this:

Error running bowtie:
Too few quality values for read: 27T3;
are you sure this is a FASTQ-int file?
Name: 27T3;
Seq: GNTCAGNTCACTCCTGGTCAAAAGAGAAAACNGCAANTTAGTCCCGCTT (49)
Qual: (0)
terminate called after throwing an instance of 'int'

from the report we could see that this sequence have no quality score. I translate the base space sequence to color space sequence and then searched it in fastq file. but the sequence could not be found. What's more, the lenth of sequence also confused me because the sra file report a lenth of 50 bases. but this sequence is 49 bases. I add the '--library-type fr-secondstrand' in tophat command but the err still there.



Anyone have suggestions? I have write a python script to exam the consistency of sequence length and quality in fastq file. but did not find anything wrong. I use tophat2. the error also exist when switch to tophat1

[Luyi Tian]

Anyone knows if tophat could analyze data from AB Solid.

[lzsph]

Hi Luyi,

On the manual page of TopHat, it says " In TopHat 1.1.0, we began supporting Applied Biosystems' Colorspace format."

Personally, I'm not familiar with Colorspace format.

Regards,
Senhao

Anyone knows if tophat could analyze data from AB Solid.

[Chirag]

Did you guys solve this problem ? I am also having similar one.

Mapping left_kept_reads_seg3 to genome mm9_c with Bowtie (3/3)
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'


cheers
Chirag

[Triple_W]

I got an error when I try to use tophat analysing Solid data from:

http://www.ncbi.nlm.nih.gov/sra/?term=SRR545797

and the err report is:


but I don't understand the read-name '32T3@'. the format of my fastq is like this:

So I tracked down the source code of bowtie and rewrite and rebuild the err report function so that it could also report the sequence and quality scores. Then my err report turned to this:


from the report we could see that this sequence have no quality score. I translate the base space sequence to color space sequence and then searched it in fastq file. but the sequence could not be found. What's more, the lenth of sequence also confused me because the sra file report a lenth of 50 bases. but this sequence is 49 bases. I add the '--library-type fr-secondstrand' in tophat command but the err still there.



Anyone have suggestions? I have write a python script to exam the consistency of sequence length and quality in fastq file. but did not find anything wrong. I use tophat2. the error also exist when switch to tophat1

I also met the error, anyone solved it?
[2013-05-17 02:36:07] Mapping left_kept_reads to transcriptome genes with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 1T2=
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'

[jtsang]

Same here, anyone has solved this problem?

[2013-12-10 02:46:57] Mapping left_kept_reads to transcriptome known with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 2013
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'

[apredeus]

I've figured out what is causing the problem (just like most people here I think, I'm trying to make use of UW mouseENCODE data)

The problem is that prep_reads (a utility in tophat package that filters off the reads that do not satisfy certain basic quality requirements) for some reason chops off the quality string, making it shorter that in the initial fastq file. Interestingly, for me, it only happens when you use exact same options as used in tophat run.log; if you run it without any extra flags the qualities string remains untouched.

I'll post here once I've gotten to the bottom of this.

[intregen]

Were you able to find a solution? I'm having similar problem.