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

Question

[Holly]

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

[Arun]

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

[Holly]

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

[Holly]

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

Answer 1

[Kieren Lythgow]

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

[Holly]

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

[Kieren Lythgow]

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

[Holly]

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.

[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. ???