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Forum: RNA Sequencing 01-10-2011, 07:01 AM
Replies: 11
Views: 4,706
Posted By anjana.vr
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...
Forum: RNA Sequencing 10-18-2010, 11:20 AM
Replies: 1
Views: 2,400
Posted By anjana.vr
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...
Forum: Bioinformatics 08-17-2010, 10:12 AM
Replies: 2
Views: 3,491
Posted By anjana.vr
Did you check the permissions? It should have...

Did you check the permissions?
It should have execute permission on all the directories leading to the file.
Forum: SOLiD 07-29-2010, 12:35 PM
Replies: 4
Views: 2,529
Posted By anjana.vr
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...
Forum: RNA Sequencing 06-22-2010, 01:37 PM
Replies: 11
Views: 4,706
Posted By anjana.vr
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...
Forum: SOLiD 06-21-2010, 02:08 PM
Replies: 2
Views: 3,072
Posted By anjana.vr
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...
Forum: RNA Sequencing 06-18-2010, 12:24 PM
Replies: 11
Views: 4,706
Posted By anjana.vr
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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