Forum: Bioinformatics
10-22-2010, 11:27 AM
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Replies: 13
Views: 6,061
Hi marcowanger,
The cufflinks compatible...
Hi marcowanger,
The cufflinks compatible file doesn't include the clipped part of the alignments. Since some alignments might be not be able to find the other end of the split read, we still keep...
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Forum: Bioinformatics
10-21-2010, 01:34 PM
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Replies: 13
Views: 6,061
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Forum: Bioinformatics
10-20-2010, 11:23 AM
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Replies: 13
Views: 6,061
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Forum: Bioinformatics
10-10-2010, 06:01 PM
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Replies: 1
Views: 1,300
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Forum: Bioinformatics
09-21-2010, 10:11 AM
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Replies: 2
Views: 2,862
Yes the nucleotide distribution is useful.
...
Yes the nucleotide distribution is useful.
If the distribution seems "uneven" at the beginning, that could indicate some residual adaptor sequences. The unevenness should be obvious when you...
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Forum: Bioinformatics
09-21-2010, 10:08 AM
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Replies: 1
Views: 1,472
If you use the sort command suggested by...
If you use the sort command suggested by cufflinks
Something like this (it should be printed out when it gives the sorting error):
sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted
Then it will...
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Forum: RNA Sequencing
09-16-2010, 03:49 PM
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Replies: 2
Views: 2,941
Hi,
The strand info will only be on the...
Hi,
The strand info will only be on the junction reads. It is impossible to determine the strand of non-junction hits without using a stranded protocol in the experiment.
column 2 is the SAM...
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Forum: Bioinformatics
09-07-2010, 03:34 PM
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Replies: 0
Views: 2,686
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Forum: Bioinformatics
09-04-2010, 02:13 PM
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Replies: 2
Views: 2,342
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Forum: Bioinformatics
09-03-2010, 01:46 PM
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Replies: 8
Views: 2,032
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Forum: Bioinformatics
08-27-2010, 11:17 AM
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Replies: 8
Views: 3,799
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Forum: Bioinformatics
08-25-2010, 02:07 PM
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Replies: 16
Views: 7,259
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Forum: Bioinformatics
08-25-2010, 01:22 PM
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Replies: 19
Views: 8,535
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Forum: Bioinformatics
08-25-2010, 12:49 PM
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Replies: 19
Views: 8,535
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Forum: Bioinformatics
08-24-2010, 11:30 AM
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Replies: 3
Views: 1,809
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Forum: Bioinformatics
08-24-2010, 11:26 AM
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Replies: 11
Views: 4,495
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Forum: Bioinformatics
08-23-2010, 12:42 PM
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Replies: 4
Views: 3,293
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Forum: Bioinformatics
08-23-2010, 12:40 PM
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Replies: 15
Views: 17,399
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Forum: Bioinformatics
08-19-2010, 01:20 PM
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Replies: 5
Views: 2,351
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Forum: Bioinformatics
08-18-2010, 07:24 PM
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Replies: 14
Views: 3,756
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Forum: Bioinformatics
08-18-2010, 12:05 PM
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Replies: 14
Views: 3,756
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Forum: Bioinformatics
08-12-2010, 11:42 AM
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Replies: 19
Views: 8,535
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Forum: Bioinformatics
08-08-2010, 10:51 AM
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Replies: 3
Views: 3,675
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Forum: Bioinformatics
08-07-2010, 10:49 PM
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Replies: 3
Views: 3,675
I thought it did this by default?
from the...
I thought it did this by default?
from the manual:
By default, if the best hit is no so repetitive (controlled by -R), BWA also finds all hits contains one more mismatch; otherwise, BWA finds...
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Forum: Bioinformatics
08-05-2010, 11:59 AM
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Replies: 12
Views: 3,811
I'm not sure what could be wrong.
Could you...
I'm not sure what could be wrong.
Could you send me your output from the command line and your "run.cfg" and i'll take a look.
Also, which version of SpliceMap are you using?
You can email...
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