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7.0 years ago
saj98
▴
140
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
Try:
And:
Both commands should return the same number of lines.
Just because:
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
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:
Returns
3908 hsapiens1.fq
Returns
3904 hsapiens2.fq
Or:
Which returns:
Please use the![101010 Button](http://i66.tinypic.com/33kdnjt.png)
code
button to format code, commands and such.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 timeAre you sure that it runs successfully? What is the last entry in the output log?
Does running tophat2 resolve the problem?