Hi All,
I have trouble using tophat with files downloaded from SRA.
My command is:
./tophat -C -p 5 -o ./825tophat ../bowtie-0.12.7/indexes/ath_gmc_colspace_110510 ~/SRR039825.fastq
Error encountered parsing file /home/SRR039825.fastq:
Length mismatch between sequence and quality strings for SRR039825.1 923_6_55 (36 vs 36).
The sequence is here:
@SRR039825.1 923_6_55
T00310202021210203103230203233012210
+
!;>1<998495<<3$4.40%/87-101*&3,8#%'#
I dig into the code, and find the problem is at line 931-934 of tophat.py, where the length of the sequence has to be 1 character longer than the quality score.
Why is this and how can I fix it?
Thanks,
Song Li
I have trouble using tophat with files downloaded from SRA.
My command is:
./tophat -C -p 5 -o ./825tophat ../bowtie-0.12.7/indexes/ath_gmc_colspace_110510 ~/SRR039825.fastq
Error encountered parsing file /home/SRR039825.fastq:
Length mismatch between sequence and quality strings for SRR039825.1 923_6_55 (36 vs 36).
The sequence is here:
@SRR039825.1 923_6_55
T00310202021210203103230203233012210
+
!;>1<998495<<3$4.40%/87-101*&3,8#%'#
I dig into the code, and find the problem is at line 931-934 of tophat.py, where the length of the sequence has to be 1 character longer than the quality score.
Why is this and how can I fix it?
Thanks,
Song Li
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