fastq file from fast-dump -split-3 contains no quality score info

Question

[colonppg]

Folks:

I ran fastdump split-3 and got fastq files

when I run tophat:

tophat-2.0.9.Linux_x86_64/tophat \
  -r 150 \
  -p 3 \
  --solexa1.3-quals \
  --fusion-search \
  -o ./tmp \
  --GTF ./genomes/human/annotation/Homo_sapiens.GRCh37.68.fix.gtf \
  ./genomes/human/hg19 \
  ./SRR1265510_1.fastq ./SRR1265510_2.fastq &

Got error message:

Error running 'prep_reads'
terminate called after throwing an instance of 'int'

I was surprised to find the .fastq files I got from split-3 does not have qc format information...

head SRR1265510_1.fastq
@SRR1265510.1 1 length=101
AGGGCATCTCTGGGAAAGGACCTGGGGCTGGTGAGGGGCCCGGAGGAGCCTTTGCCCGCGTGTCAGACTCCATCCCTCCTCTGCCGCCACCGCAGCAGCCC
+SRR1265510.1 1 length=101
@CCFFD?DHHHHGIGIIIIFHI@HICGGGHIDGGDHAEF6@FG@BE1??B;@CCAAC>>B8?&844::(4@ACAABCCBCC:4:@>99<525&&0&2?BB#
@SRR1265510.2 2 length=101
CGCAAGGGCATCTCTGGGAAAGGACCTGGGGCTGGTGACGGGCCCGGAGGAGCCTTTGCCCGCGTGTCAGACTCCATCCCTCCTCTGCCGCCACCGCAGCA
+SRR1265510.2 2 length=101
CCCFFFFFHHHHHJJJJJJJJJJIJJIJJJJJJJJAFHIJJIIJIIHHFDDDDDDDDDDDDDDD>B>BCDDDDDDCDCDDDDBACCCCCBDDDDDDDDDDB

What could be the cause of this? Shall I run fastq-dump again using --split-files?

[h.mon]

What do you mean by "does not have qc format information"? The lines in bold below are the quality score lines.

@SRR1265510.1 1 length=101
AGGGCATCTCTGGGAAAGGACCTGGGGCTGGTGAGGGGCCCGGAGGAGCCTTTGCCCGCGTGTCAGACTCCATCCCTCCTCTGCCGCCACCGCAGCAGCCC
+SRR1265510.1 1 length=101
@CCFFD?DHHHHGIGIIIIFHI@HICGGGHIDGGDHAEF6@FG@BE1??B;@CCAAC>>B8?&844::(4@ACAABCCBCC:4:@>99<525&&0&2?BB#
@SRR1265510.2 2 length=101
CGCAAGGGCATCTCTGGGAAAGGACCTGGGGCTGGTGACGGGCCCGGAGGAGCCTTTGCCCGCGTGTCAGACTCCATCCCTCCTCTGCCGCCACCGCAGCA
+SRR1265510.2 2 length=101
CCCFFFFFHHHHHJJJJJJJJJJIJJIJJJJJJJJAFHIJJIIJIIHHFDDDDDDDDDDDDDDD>B>BCDDDDDDCDCDDDDBACCCCCBDDDDDDDDDDB

[colonppg]

Thanks for your reply, what I mean is it lacks QC encoding info as the ################ section usually contains that info... this cause tophat stop working

+SRR1265510.1 1 length=101 #########################
@CCFFD?DHHHHGIGIIIIFHI@HICGGGHIDGGDHAEF6@FG@BE1??B;@CCAAC>>B8?&844::(4@ACAABCCBCC:4:@>99<525&&0&2?BB#

Answer 1

[colonppg]

tophat-2.0.9.Linux_x86_64/tophat -r 150 -p 3 -o ./tmp --GTF ./genomes/human/annotation/Homo_sapiens.GRCh37.68.fix.gtf ./genomes/human/hg19 ./SRR1265510_1.fastq ./SRR1265510_2.fastq &

tophat started working without the --solexa1.3, I guess this is probably not good without considering quality score coding...