tophat: option --read-gap-length not recognized?

[eric.yu]

Hi,

I'm really new to this so please bear with me if I made some really silly mistakes.

Here's my code for tophat:
tophat -p 8 --bowtie1 -G path --no-novel-juncs --read-mismatches 4 --read-gap-length 3 --read-edit-dist 2 -o path path &

and it gave me error :
tophat: option --read-gap-length not recognized

Any advice'd be appreciated thanks!

[chadn737]

1) What version of tophat are you running.....are you sure you have tophat2? Try typing tophat --version to see what version you have.

2) Secondly, that command wouldn't work anyhow. --read-mismatches and --read-gap-length cannot exceed the value of --read-edit-dist. If you want to set the read-mismatches to 4 an --read-gap-length to 3, then you also have to set the read-edit-dist to 4 or more.

[eric.yu]

Originally Posted by chadn737

1) What version of tophat are you running.....are you sure you have tophat2? Try typing tophat --version to see what version you have.

2) Secondly, that command wouldn't work anyhow. --read-mismatches and --read-gap-length cannot exceed the value of --read-edit-dist. If you want to set the read-mismatches to 4 an --read-gap-length to 3, then you also have to set the read-edit-dist to 4 or more.

Thanks for your reply.
It's 2.0.4
and also tried
tophat -p 8 --bowtie1 -G $home/Genes/genes.gtf --no-novel-juncs --read-mismatches 4 --read-gap-length 3 --read-edit-dist 4 -o $home/C1_thout3 $home/BowtieIndex/genome $home/Sample_C1.R1_trimmed.fq.gz &

still doesn't run

[jp.]

Hi Senior Member
I have used tophat successfully with default functions. however, this time I got problem. How to give commands for read length 101 x 2 with insert sixe 80~380(main 150) ?
I am totally confused

Originally Posted by chadn737

1) What version of tophat are you running.....are you sure you have tophat2? Try typing tophat --version to see what version you have.

2) Secondly, that command wouldn't work anyhow. --read-mismatches and --read-gap-length cannot exceed the value of --read-edit-dist. If you want to set the read-mismatches to 4 an --read-gap-length to 3, then you also have to set the read-edit-dist to 4 or more.

[westerman]

Originally Posted by jp.

Hi Senior Member
I have used tophat successfully with default functions. however, this time I got problem. How to give commands for read length 101 x 2 with insert sixe 80~380(main 150) ?
I am totally confused

I presume that you've looked at --mate-inner-distance plus --mate-std-dev and are just having a hard time figuring out that the numbers should be. Here are two relevant seqanswer posts that should help:

http://seqanswers.com/forums/showthread.php?t=4815

and

http://seqanswers.com/forums/showthread.php?t=4355

[jp.]

Thank you so much for your help. I got the answer. negative value can be given for --mate-inner-distance.
Great help for me, thanks

Originally Posted by westerman

I presume that you've looked at --mate-inner-distance plus --mate-std-dev and are just having a hard time figuring out that the numbers should be. Here are two relevant seqanswer posts that should help:

http://seqanswers.com/forums/showthread.php?t=4815

and

http://seqanswers.com/forums/showthread.php?t=4355