Hi Benjy,
To extract unmapped reads from a SAM file in Galaxy, you can use 'Filter
SAM' ('NGS: SAM Tools' - 'Filter SAM'). Add a 'flag' and use the 'The read
is unmapped' type, then set the state for this flag to 'Yes'. This should
return a SAM file with your unmapped reads.
Cheers,
Mo
Hi Thanh,
This is due to Cuffdiff correcting for the size of smaller transcripts, the
authors call it the effective length correction. It is supposed to
correct the loss of shorter transcripts upon size selection in creating
your RNA-seq library. The default setting on Galaxy is to use the
:
On Jul 8, 2013, at 3:50 PM, Mohammad Heydarian wrote:
Hi,
I am having trouble setting up a FTP connection with the recently
released version of Galaxy Cloudman (ami-118bfc78).
I have instantiated the new version of Galaxy Cloudman with CloudLaunch
and also through the AWS EC2 wizard
We are having the exact same issue, on the main server and our (recent)
cloud instances.
Were some of the hidden Cuffdiff parameters modified since fall 2012?
Cheers,
Mo Heydarian
On Mar 13, 2013 11:02 AM, Jenna Smith jes...@case.edu wrote:
Hi,
I'll preface my concern by saying that I'm a
Hi,
I am using the Count intervals in one file overlapping intervals in
another file tool (part of the bedTools package) to assess the number of
RNA-seq reads that map back to a specific region. (I am using this on the
Galaxy test server). I am finding that this tool returns many more reads
than
Hello,
Is there a way to generate a pile-up from a BAM file in SAMtools without
including spliced (intronic) regions? Alternatively, is there a way to
split spliced reads in a BAM file?
Thanks in advance!
Cheers,
Mo Heydarian
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