I am new to tophat2 and when I ran the tophat2 command:
"tophat2 --b2-very-fast -p 8 /home/mbashyam/indexes/hg19index /home/mbashyam/reads/SRR222177.fastq"
it gave an error initially:
"Warning: Could not find FASTA file /home/mbashyam/indexes/hg19index.fa
[2013-01-30 18:32:46] Reconstituting reference FASTA file from Bowtie index"
But the program moved on with the alignment (and is still running).
I have used the same index files for bowtie2 earlier so I know they are ok. I would be grateful if someone could explain this error; or maybe it is to be ignored?
"tophat2 --b2-very-fast -p 8 /home/mbashyam/indexes/hg19index /home/mbashyam/reads/SRR222177.fastq"
it gave an error initially:
"Warning: Could not find FASTA file /home/mbashyam/indexes/hg19index.fa
[2013-01-30 18:32:46] Reconstituting reference FASTA file from Bowtie index"
But the program moved on with the alignment (and is still running).
I have used the same index files for bowtie2 earlier so I know they are ok. I would be grateful if someone could explain this error; or maybe it is to be ignored?
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