Hi,
I used the Megablast function (in the NGS: Mapping\ROCHE-454\) to
analyze my FASTA sequences against nt database and it worked fine for
me. However, it generated 56,804 hits although my query has only 1000
sequences. I am wondering is there any way to suppress the number of
reported alignments
Daniel:
To get a good idea on how Galaxy handles so called interval operations take a
look at http://usegalaxy.org/galaxy101.
The answer to your question depends on what you would like to do. Are
interested in obtaining the read coverage for a set of genes or simply
identifying a set of reads
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]）:+ ?
Be
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
抄送：
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 wrote:
> Thank you very much for your reply!
>
> I'd like to know ho
Hi,
I have reads from Illumina paired-end run mapped against reference genome using
Bowtie. Is there a Galaxy tool which would allow me to extract gene names from
the mapped chromosomal regions? In this case I have cat genome, example of the
output row is bellow.
Thanks for anymhelp,
Daniel
HWUS
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 w
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
specif
> On Thu, Mar 10, 2011 at 7:55 AM, Jeremy Goecks
> 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 cuffdiff.
>> 2.
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] Inspect
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