Forum: RNA Sequencing
01-10-2011, 07:01 AM
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Replies: 11
Views: 4,706
Hi whfwind,
The problem was that the schema...
Hi whfwind,
The problem was that the schema 18_2 was not present. I did ask the ABI FAs for that schema but then I realized that I only needed 18_1 schema.
Check in the schema directory and see...
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Forum: RNA Sequencing
10-18-2010, 11:20 AM
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Replies: 1
Views: 2,400
Differential gene expression of gene clusters
Hi
I am analyzing RNA-Seq data. I have RPKM values for all the genes. The data set contains 7 samples. I am looking into genes associated with a specific pathway. This pathways has 6 gene...
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Forum: Bioinformatics
08-17-2010, 10:12 AM
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Replies: 2
Views: 3,491
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Forum: SOLiD
07-29-2010, 12:35 PM
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Replies: 4
Views: 2,529
The SOLiD itself has a small RNA pipeline. It...
The SOLiD itself has a small RNA pipeline. It takes into account the fact that reads from miRNA have the RNA + the adaptors. If the mappers you tried failed because of the small read size then I...
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Forum: RNA Sequencing
06-22-2010, 01:37 PM
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Replies: 11
Views: 4,706
Thanks Fennan. I am running with split read...
Thanks Fennan. I am running with split read length 25 now. It is taking forever to run it. The first time it was at extension phase (after 2 days). I stopped it and I am running it again. Hopefully...
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Forum: SOLiD
06-21-2010, 02:08 PM
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Replies: 2
Views: 3,072
Looks like the file is in .ma format. Its...
Looks like the file is in .ma format. Its something that SOLiD uses frequently. I have this description of the format.
>bead_ID, sequence#_signedCoordinate_#mm_alignmentSize .
Also you can...
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Forum: RNA Sequencing
06-18-2010, 12:24 PM
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Replies: 11
Views: 4,706
hi Adam,
I am trying to use splitseek for...
hi Adam,
I am trying to use splitseek for novel junction detection. After running split_read_mapper I get the following error
SEVERE: Schema file /WT/ab_wtp_v1.2.1/etc/schemas/schema_18_2_adj...
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