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Hi：
I use the solid PE sequencing data and mapped with the bioscope tools(AB
company supported) ，which is better for solid data mapping ,so I don't use the
bowtie to map . Ｉgain the BAM file! Now ,I want use the cufflinks to calculate
the gene expression. But there is a error.
[15:08:06]
On Thu, Mar 10, 2011 at 7:55 AM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
Jagat,
Just like any mRNA-seq experiment to achieve following objectives:
1. Reconstruct all transcripts of a particular gene and corresponding
Cuffdiff significantly expressed transcripts as called by
Hi Li,
Tophat includes a custom tag 'XS' at the end of spliced read alignments
which your pipeline is not aware about.
The following is taken from http://cufflinks.cbcb.umd.edu/manual.html
Cufflinks takes a text file of SAM alignments as input. For more details on
the SAM format, see the
Cufflinks requires an 'xs' tag on each read in the bam file. Only tophat does
this. You can write a script to add this or remap with tophat.
How much of a difference do you see between tophat and bioscope?
Please excuse any typos -- Sent from my iPhone
On Apr 11, 2011, at 9:46 AM, lishiyong
Since SOLiD reads are strand-specific you can use the option '--library-type
fr-secondstrand', and the strand information will automatically be added to
the reads during the run.
-Adam
On Mon, Apr 11, 2011 at 8:27 AM, gaohuan gaoh...@genomics.org.cn wrote:
Thank you very much for your reply!
Thank you very much for your reply!
I'd like to know how to add this 'xs' tag since the amount of reads mapped to
genome is much less using tophat, can we just add a '+' or '-' at the end of
each line?
2011-04-11
gaohuan
发件人： Ryan Golhar
发送时间： 2011-04-11 23:19:10
收件人： lishiyong
Hi,Paul Korir:
Thank you for yours help.I have known the reason,But I also I have a little
problem about to solve the question.
if I want to add a XS tag ,what should I do ,can you tell me in detail(like
that ,dose it only have two value ,such as XS:A:-,XS:A:+ ,not have
XS:B（[B-Z]）:+ ?
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