tophat2

mdb@wistar · 01-30-2013, 03:56 PM

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 · 02-01-2013, 08:10 AM

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 · 02-01-2013, 08:13 AM

Quote:

Originally Posted by 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

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 · 02-01-2013, 08:16 AM

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 · 02-01-2013, 08:28 AM

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

Jetse · 02-04-2013, 02:50 AM

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 · 02-04-2013, 11:51 AM

Thanks, I got it now

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01-30-2013, 03:56 PM	#1
mdb@wistar Junior Member Location: new jersey Join Date: Jan 2013 Posts: 9	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?

02-01-2013, 08:10 AM	#2
Jetse Member Location: The netherlands Join Date: Nov 2012 Posts: 38	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

02-01-2013, 08:16 AM	#4
Jetse Member Location: The netherlands Join Date: Nov 2012 Posts: 38	This warning disappears when the name of the fasta file is the same as the name of the index (both without the suffixes.

02-01-2013, 08:28 AM	#5
mdb@wistar Junior Member Location: new jersey Join Date: Jan 2013 Posts: 9	Thanks. I am sorry I did not follow your comment. Which fasta file?

02-04-2013, 02:50 AM	#6
Jetse Member Location: The netherlands Join Date: Nov 2012 Posts: 38	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.

02-04-2013, 11:51 AM	#7
mdb@wistar Junior Member Location: new jersey Join Date: Jan 2013 Posts: 9	Thanks, I got it now