[DerSeb]

@jamessmith01, Cufflinks just reports the shortest length read it finds.

Be on the lookout for the next version of Cufflinks (hopefully coming this week), which will include proper options to handle strand-specificity in the SOLiD protocol.

All right, i just tried cufflinks as well and was irritated by the read length of 25bp as well. thx for letting me know!

[agc]

Version 1.1.1 on the main page apparently includes fixes for these bugs...

I'm using TopHat version 1.1.4 with bowtie version 0.12.7.0, and getting the following error with two out of four samples:

  File "~/Tools/TopHat/tophat-1.1.4.Linux_x86_64/tophat", line 1520, in convert_color_to_bp
    base = decode_dic[base+ch]
KeyError: 'CN'

Where in one sample the error is 'CN' (as above) and in the other it's 'GN'. I'm using a SOLiD csfasta file and quals file with the command:

~/Tools/TopHat/tophat-1.1.4.Linux_x86_64/tophat -p 5 --library-type fr-secondstrand -CQ ~/References/bowtie-hg19/hg19-bowtie-cs sample_1_F3.csfasta samples_1_F3_QV.qual

While many others had this issue, it seems that it should have been solved in the new version.

[Daehwan]

Hi agc,

I just fixed this "N" bug and the next version will include the fix.

Daehwan

[AdamB]

Hi,

Please can anyone who has used TopHat with SOLiD strand-specific data, say whether you used the fr-firststrand, fr-secondstarand or neither option?

To be clear, I'm using paired-end (50+25 bp), strand-specific SOLiD RNA-sequencing reads, and would like to know which option, if any, to use.

Thanks.

[adarob]

fr-secondstrand

See here: http://cufflinks.cbcb.umd.edu/manual.html#library

[AdamB]

Thanks adarob.

Do you know where I can find the mapping stats from the TopHat run (% mapped, % paired, etc)? I saw them in the individual logs, but not all collected in one file.

Thanks.