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Dear All,
I am new to the RNASeq data analysis and I have a query regarding TopHat for, RNASeq data containing paired-end reads, some specific options to be used.
I am using TopHat v2.0.10 on ubuntu and it works fine and gives the output files with default options but when I use the options "--no-discordant" and "--no-mixed" to get more specific outcomes I get an error at the stage of "tophat_reports" with a message like this.
[FAILED]
Error running tophat_reports
Loaded ****** junctions
I tried searching to see if someone else had the same problem and then I found a suggestion that v2.0.9 works with these options but after testing it I found the same error at the stage of "tophat_reports".
It will be very nice if anyone could please help me if there is something that I am doing wrong? This is the way I am using it:
tophat2 -p 8 -G genes.gtf --no-discordant --no-mixed -o output_dir genome reads1.fq reads2.fq
I also tried with only one option at a time like using "--no-mixed" and only using "--no-discordant":
tophat2 -p 8 -G genes.gtf --no-mixed -o output_dir genome reads1.fq reads2.fq
tophat2 -p 8 -G genes.gtf --no-discordant -o output_dir genome reads1.fq reads2.fq
The tophat run process with the --no-mixed option works fine in both v2.0.10 and v2.0.9 also but the tophat run process with the --no-discordant option fails in both the versions with the same error as mentioned above. So I am guessing that there is some issue with using the --no-discordant option.
Is there some other version which works with these options together or only with the --no-discordant option or is there something that I can fix to overcome the error so that the process can be completed with the --no-discordant option?
Thank You
Regards,
Pawan
I am new to the RNASeq data analysis and I have a query regarding TopHat for, RNASeq data containing paired-end reads, some specific options to be used.
I am using TopHat v2.0.10 on ubuntu and it works fine and gives the output files with default options but when I use the options "--no-discordant" and "--no-mixed" to get more specific outcomes I get an error at the stage of "tophat_reports" with a message like this.
[FAILED]
Error running tophat_reports
Loaded ****** junctions
I tried searching to see if someone else had the same problem and then I found a suggestion that v2.0.9 works with these options but after testing it I found the same error at the stage of "tophat_reports".
It will be very nice if anyone could please help me if there is something that I am doing wrong? This is the way I am using it:
tophat2 -p 8 -G genes.gtf --no-discordant --no-mixed -o output_dir genome reads1.fq reads2.fq
I also tried with only one option at a time like using "--no-mixed" and only using "--no-discordant":
tophat2 -p 8 -G genes.gtf --no-mixed -o output_dir genome reads1.fq reads2.fq
tophat2 -p 8 -G genes.gtf --no-discordant -o output_dir genome reads1.fq reads2.fq
The tophat run process with the --no-mixed option works fine in both v2.0.10 and v2.0.9 also but the tophat run process with the --no-discordant option fails in both the versions with the same error as mentioned above. So I am guessing that there is some issue with using the --no-discordant option.
Is there some other version which works with these options together or only with the --no-discordant option or is there something that I can fix to overcome the error so that the process can be completed with the --no-discordant option?
Thank You
Regards,
Pawan
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