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Old 01-30-2013, 03:56 PM   #1
mdb@wistar
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Default tophat2

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?
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Old 02-01-2013, 08:10 AM   #2
Jetse
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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
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Old 02-01-2013, 08:13 AM   #3
mdb@wistar
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Quote:
Originally Posted by Jetse View Post
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.
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Old 02-01-2013, 08:16 AM   #4
Jetse
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This warning disappears when the name of the fasta file is the same as the name of the index (both without the suffixes.
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Old 02-01-2013, 08:28 AM   #5
mdb@wistar
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Thanks. I am sorry I did not follow your comment. Which fasta file?
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Old 02-04-2013, 02:50 AM   #6
Jetse
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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.
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Old 02-04-2013, 11:51 AM   #7
mdb@wistar
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Thanks, I got it now
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