Tophat software error

Question

[saj98]

Hello every one I used the following tophat command to get thout file.

tophat -p 5 -o WS001_R1_thout --library-type=fr-firststrand -G Documents/Shaima/Seq/Pros/S/Rn6/Rn6.gtf 
Documents/Shaima/Seq/Pros/S/Rn6/Rn6_index Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R1_001.fastq 
Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R2_001.fastq

The program run successfully, but then gave me the following error:

Error: failed to retrieve right read for pair # 8885216 !

Appreciate your help

[h.mon]

Try:

wc -l Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R1_001.fastq

And:

wc -l Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R2_001.fastq

Both commands should return the same number of lines.

[Ram]

Just because:

[[ $(wc -l Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R1_001.fastq | cut -d" " -f1) -eq \
    $(wc -l Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R2_001.fastq | cut -d" " -f1) ]] \
    || echo "FASTQ files do not have an equal number of reads"

[saj98]

Hello Thank you so much for your help, I tried to follow your command, but I got the following error. Could you please check my mistake. I appreciate your time $ tophat -p 10 -o WS001_R1_thout --library-type=fr-firststrand -G Documents/Shaima/Seq/Pros/S/Rn6/Rn6.gtf Documents/Shaima/Seq/Pros/S/Rn6/Rn6_index Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R1_001.fastq | cut -d" " -f1 -eq \ Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R2_001.fastq | cut -d" " -f1

The error I got is: cut: invalid option -- 'e' Try 'cut --help' for more information.

Thanks for help

[h.mon]

I think you completely misunderstood my and Ram suggestions, though I am not sure as your post is unreadable without proper code formatting.

We are just pointing to the fact you may have a different number of reads in your R1 and R2 files, and gave you two methods of testing it. You are not supposed to insert the commands we gave into your Tophat command, you have to issue them on their own, for example:

wc -l hsapiens1.fq

Returns 3908 hsapiens1.fq

wc -l hsapiens2.fq

Returns 3904 hsapiens2.fq

Or:

[[ $(wc -l hsapiens1.fq | cut -d" " -f1) -eq \
    $(wc -l hsapiens2.fq | cut -d" " -f1) ]] \
    || echo "FASTQ files do not have an equal number of reads"

Which returns:

FASTQ files do not have an equal number of reads

Please use the code button to format code, commands and such.

[saj98]

I am so sorry for misunderstood, I did the following command

The command: $ wc -l Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R1_001.fastq Then I got the following: 472646376 Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R1_001.fastq The the second line: $ wc -l Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R2_001.fastq Which gave me: 472646376 Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R2_001.fastq I appreciate your time

[Kevin Blighe]

Are you sure that it runs successfully? What is the last entry in the output log?

Does running tophat2 resolve the problem?