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Tophat Error: No Such File Or Directory: 'S_1_Sequence.Fq'

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

tophat
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updated by Biostar Biostar • written by Holly • Holly

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

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written by Arun Arun

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

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written by Holly • Holly

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

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written by Holly • Holly

1 answer

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

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written by Kieren Lythgow • Kieren Lythgow

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

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written by Holly • Holly

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

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written by Kieren Lythgow • Kieren Lythgow

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.

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written by Holly • Holly

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. ???

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written by Holly • Holly

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