Question: Tophat Error: No Such File Or Directory: 'S_1_Sequence.Fq'
0
gravatar for Holly
8.1 years ago by
Holly30
United States
Holly30 wrote:

new to tophat...any idea where the datafiles need to be for the program to recognize? The test files ran fine. thanks

tophat • 1.8k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 8.1 years ago by Holly30

what is the command you typed? and where is s_1_sequence.fq located?

ADD REPLYlink written 8.1 years ago by Arun2.3k

I unpacked my reference index and two sequence files in my data folder 'human_test' command entered

tophat -r 20 /wikihomedir/hmortens/Humantest/hg18c s1sequence.fq s2sequence.fq

ADD REPLYlink written 8.1 years ago by Holly30

i think this may be a memory error from what I see others experiencing.

ADD REPLYlink written 8.1 years ago by Holly30
1
gravatar for Kieren Lythgow
8.1 years ago by
Southampton
Kieren Lythgow110 wrote:

You have an uppercase H in your path. It's not a memory issue.

ADD COMMENTlink written 8.1 years ago by Kieren Lythgow110

thanks ! once I remove the H, I get the following error: Could not find Bowtie index files /wikihomedir/hmortens/human_test/hg18_c.*

ADD REPLYlink written 8.1 years ago by Holly30

You need to install the downloaded archive into the indexes subdirectory in your Bowtie installation as this is where it looks for the archives.

ADD REPLYlink written 8.1 years ago by Kieren Lythgow110

can you tell me if y ou put your input sequence datafiles in the same directory? After moving my indexes to the index file as you suggested, I still get the 'no such file in directory' error. many thanks for your help.

ADD REPLYlink written 8.1 years ago by Holly30

duh.. got it. thanks. on to the next error! Error: qual length (60) differs from seq length (35) for fastq record ! using two seq files from Pickrell for testing. ???

ADD REPLYlink written 8.1 years ago by Holly30
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