tophat2

[mdb@wistar]

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?

[Jetse]

You don't have a fasta file with the same name as the bowtie index.
Tophat is only a little bit slower, because it makes an extra step by creating this reference fasta file. Nothing to worry about

[mdb@wistar]

You don't have a fasta file with the same name as the bowtie index.
Tophat is only a little bit slower, because it makes an extra step by creating this reference fasta file. Nothing to worry about

Thanks. My index file which I made for bowtie2 was called hg19.fa; my colleague renamed it to hg19index.fa and then the error disappeared.

[Jetse]

This warning disappears when the name of the fasta file is the same as the name of the index (both without the suffixes.

[mdb@wistar]

Thanks. I am sorry I did not follow your comment. Which fasta file?

[Jetse]

The fasta file from which the bowtie index is made. When you have downloaded the bowtie index, and not created the bowtie index from a fasta file, you always get this warning.

[mdb@wistar]

Thanks, I got it now