Dear All,
I have downloaded some data from SRA (SRP011410), which were on an ABI SOLiD4 (50bp RNAseq reads).
I am trying to align the reads to the Ensembl TAIR10 reference genome with bowtie 1 and I get the following error:
In order to get to that stage, I:
1) I converted the SRA data to .csfata and .quals files using the abi-dump (v2.8.2) command from the sra toolkit.
2) I used the Ensembl TAIR10 genome to build the colorspace indexes for bowtie 1, using the command:
3) I ran the following code for tophat2:
I appreciate any help that you can give me to solve this issue!!!
Thank you very much!
Best regards,
Andres
I have downloaded some data from SRA (SRP011410), which were on an ABI SOLiD4 (50bp RNAseq reads).
I am trying to align the reads to the Ensembl TAIR10 reference genome with bowtie 1 and I get the following error:
Code:
[2018-02-13 18:59:36] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2018-02-13 18:59:36] Checking for Bowtie Bowtie version: 1.2.2.0 [2018-02-13 18:59:36] Checking for Bowtie index files (genome).. [2018-02-13 18:59:36] Checking for reference FASTA file [2018-02-13 18:59:36] Generating SAM header for genome-color [2018-02-13 18:59:37] Preparing reads left reads: min. length=50, max. length=50, 43369633 kept reads (234454 discarded) [2018-02-13 19:08:20] Mapping left_kept_reads to genome genome-color with Bowtie [FAILED] Error running bowtie: Reads file contained a pattern with more than 1024 quality values. Please truncate reads and quality values and and re-run Bowtie terminate called after throwing an instance of 'int'
1) I converted the SRA data to .csfata and .quals files using the abi-dump (v2.8.2) command from the sra toolkit.
2) I used the Ensembl TAIR10 genome to build the colorspace indexes for bowtie 1, using the command:
Code:
bowtie-build -C genome.fa
Code:
tophat2 -p 8 -I 5000 --bowtie1 --color --quals --library-type=fr-secondstrand -o <output_dir> genome-color <csfasta file> <quals file>
Thank you very much!
Best regards,
Andres
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