Hi all,
I am trying to use tophat to map SOLiD colorspace pair-end (50x35) reads with tophat. However, when I tried with the standard procedure which looks something like:
I got the following error:
I checked and re-checked many things regarding my file formats and checked the logs. Eventually, I found that the tophat wrapper is launching prep_reads which does not produce fasta output (rather fastq output), while the subsequent bowtie command assumes fasta format from stdin. So what I did was to edit tophat.py, and commented out the lines 2164-2165
and saved to my_tophat.py in order to use specifically with my data.
This was not of course the right way to do, so my question is, am I doing something wrong, or somebody else here has encountered this before. Is it a tophat bug?
Thanks!
I am trying to use tophat to map SOLiD colorspace pair-end (50x35) reads with tophat. However, when I tried with the standard procedure which looks something like:
Code:
tophat --color --quals --num-threads 8 --coverage-search --library-type fr-secondstrand --output-dir ./tophat_out --prefilter-multihits --keep-tmp --GTF /opt/iGenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --bowtie1 /opt/NGSTools/Bowtie/indexes/hg19_c ./CON_BR1_F3.csfasta ./CON_BR1_F5.csfasta ./CON_BR1_F3_QV.qual ./CON_BR1_F5_QV.qual
Code:
[2012-12-20 16:07:24] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2012-12-20 16:07:24] Checking for Bowtie Bowtie version: 0.12.8.0 [2012-12-20 16:07:24] Checking for Samtools Samtools version: 0.1.18.0 [2012-12-20 16:07:24] Checking for Bowtie index files [2012-12-20 16:07:24] Checking for reference FASTA file Warning: Could not find FASTA file /opt/NGSTools/Bowtie/indexes/hg19_c.fa [2012-12-20 16:07:24] Reconstituting reference FASTA file from Bowtie index Executing: /opt/NGSTools/Bowtie/bowtie-inspect /opt/NGSTools/Bowtie/indexes/hg19_c > ./tophat_out/tmp/hg19_c.fa [2012-12-20 16:11:08] Generating SAM header for /opt/NGSTools/Bowtie/indexes/hg19_c format: fasta [2012-12-20 16:11:30] Reading known junctions from GTF file [2012-12-20 16:11:36] Pre-filtering multi-mapped left reads [2012-12-20 16:11:36] Mapping CON_BR1_F3 to genome hg19_c with Bowtie [FAILED] Error running bowtie: Error: reads file does not look like a FASTA file terminate called after throwing an instance of 'int'
Code:
#elif reads_format == "fasta": # bowtie_cmd += ["-f"]
This was not of course the right way to do, so my question is, am I doing something wrong, or somebody else here has encountered this before. Is it a tophat bug?
Thanks!
Comment