I have been trying for several weeks to run Tophat on SOLiD reads but I got the same error message every time. While I searched a lot of forums and related questions but could not find a solution.
a sample of my data is:
=====
@SRR179591.60.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_70_490_F3 length=50
T02213232.20202212300333
+SRR179591.60.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_70_490_F3 length=50
!<=B?@=7B!8>;@BB<:@-<259
=====
I use Tophat v2.0.13 and the error message that I got is:
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[2015-01-22 11:01:43] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2015-01-22 11:01:43] Checking for Bowtie
Bowtie version: 1.1.1.0
[2015-01-22 11:01:43] Checking for Bowtie index files (genome)..
[2015-01-22 11:01:43] Checking for reference FASTA file
[2015-01-22 11:01:43] Generating SAM header for HumanGenome/Ensemble78/HumanIndexedGenome/Bowtie1ColorSpace//Human
Warning: found a read < 20bp in SRR179592_Trimmed.fastq
[2015-01-22 11:02:06] Reading known junctions from GTF file
[2015-01-22 11:02:55] Preparing reads
left reads: min. length=19, max. length=50, 20533939 kept reads (147 discarded)
Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
[2015-01-22 11:08:48] Building transcriptome data files TophatAlignment/tmp/Homo_sapiens.GRCh38.78
[2015-01-22 11:10:07] Building Bowtie index from Homo_sapiens.GRCh38.78.fa
[2015-01-22 11:44:10] Mapping left_kept_reads to transcriptome Homo_sapiens.GRCh38.78 with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 1T0B
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
========
The command that I used to run Tophat is:
=====
tophat --color --bowtie1 -o out -r 500 --mate-std-dev 500 --no-mixed -p 16 -G Homo_sapiens.GRCh38.78.gtf Bowtie1ColorSpace/Human Reads_Trimmed.fastq
=====
a sample of my data is:
=====
@SRR179591.60.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_70_490_F3 length=50
T02213232.20202212300333
+SRR179591.60.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_70_490_F3 length=50
!<=B?@=7B!8>;@BB<:@-<259
=====
I use Tophat v2.0.13 and the error message that I got is:
=====
[2015-01-22 11:01:43] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2015-01-22 11:01:43] Checking for Bowtie
Bowtie version: 1.1.1.0
[2015-01-22 11:01:43] Checking for Bowtie index files (genome)..
[2015-01-22 11:01:43] Checking for reference FASTA file
[2015-01-22 11:01:43] Generating SAM header for HumanGenome/Ensemble78/HumanIndexedGenome/Bowtie1ColorSpace//Human
Warning: found a read < 20bp in SRR179592_Trimmed.fastq
[2015-01-22 11:02:06] Reading known junctions from GTF file
[2015-01-22 11:02:55] Preparing reads
left reads: min. length=19, max. length=50, 20533939 kept reads (147 discarded)
Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
[2015-01-22 11:08:48] Building transcriptome data files TophatAlignment/tmp/Homo_sapiens.GRCh38.78
[2015-01-22 11:10:07] Building Bowtie index from Homo_sapiens.GRCh38.78.fa
[2015-01-22 11:44:10] Mapping left_kept_reads to transcriptome Homo_sapiens.GRCh38.78 with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 1T0B
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
========
The command that I used to run Tophat is:
=====
tophat --color --bowtie1 -o out -r 500 --mate-std-dev 500 --no-mixed -p 16 -G Homo_sapiens.GRCh38.78.gtf Bowtie1ColorSpace/Human Reads_Trimmed.fastq
=====
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