I have converted SOLiD SRA to fasta using fastq-dump.
Then, I used the Galaxy groomer to remove the adapter. After that, I wrote a script to translate "0123." to "ACGTN" in the fasta file.
Then, I tried blasting that fasta file against the human genome, and found no significant results.
Earlier, my SAM alignment (derived from the converted fasta file and a reference .mrna human file) also showed very few hits (only 406 out of 6 million).
So, now the finding from BLAST makes me think that the conversion of the human SOLiD sra file went awry somewhere.
I got my .sra file from here (http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR452364, by downloading the "Run" HTTP file).
Based on the above information, does anyone have any ideas where I went wrong in converting the SOLiD sra file to a format ready for BLAST/SAM?
Many thanks...
Then, I used the Galaxy groomer to remove the adapter. After that, I wrote a script to translate "0123." to "ACGTN" in the fasta file.
Then, I tried blasting that fasta file against the human genome, and found no significant results.
Earlier, my SAM alignment (derived from the converted fasta file and a reference .mrna human file) also showed very few hits (only 406 out of 6 million).
So, now the finding from BLAST makes me think that the conversion of the human SOLiD sra file went awry somewhere.
I got my .sra file from here (http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR452364, by downloading the "Run" HTTP file).
Based on the above information, does anyone have any ideas where I went wrong in converting the SOLiD sra file to a format ready for BLAST/SAM?
Many thanks...
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