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Forum: RNA Sequencing 03-11-2013, 12:26 PM
Replies: 1
Views: 1,235
Posted By proteomania
RNAmmer Prediction works fine, and 5.8S was...

RNAmmer Prediction works fine, and 5.8S was intentionally excluded from the prediction, in the paper the authors wrote,

"In eukaryotes, 5S, 5.8S and 28S rRNA exist in the large subunit, and 18S...
Forum: RNA Sequencing 10-13-2012, 12:00 PM
Replies: 1
Views: 1,895
Posted By proteomania
3'End polyA artefact in illumina TruSeq Small RNA Seq

Hi All,

I've been using Illumina TruSeq Kit to prepare Small RNA libraries. I found a small RNA population (non-miRNA) has about 1 to 8 extra As at their 3'end (mismatch to genome). I was...
Forum: Bioinformatics 08-21-2012, 08:46 AM
Replies: 7
Views: 6,646
Posted By proteomania
DESeq and GSEA with pre-ranked gene list

Hi all,

I've been using DESeq for my RNA-Seq differential expression analysis. Now I want to use the DESeq result to generate a ranked-list, which will be used as the input in GSEA. My...
Forum: General 05-19-2011, 08:26 AM
Replies: 3
Views: 2,113
Posted By proteomania
If you are talking about the illumina standard...

If you are talking about the illumina standard pair-end seq, i think i should be

file1
read/1 AAAG

file2
read/2 GAGA

Our illumina data look this way. The mate are on opposite strands...
Forum: RNA Sequencing 04-27-2011, 02:15 AM
Replies: 2
Views: 1,259
Posted By proteomania
The problem was identified. The end of the second...

The problem was identified. The end of the second half of the junction somehow fell beyond the contig and the extracted contig sequence is shorter than the actual read seq and that create the...
Forum: RNA Sequencing 04-20-2011, 07:47 AM
Replies: 2
Views: 1,259
Posted By proteomania
Somehow I've found this error can be resolved by...

Somehow I've found this error can be resolved by increasing the 2nd half anchor value. Any ideas?
Forum: RNA Sequencing 04-19-2011, 02:42 AM
Replies: 2
Views: 1,259
Posted By proteomania
HMMSplicer "_scoreHalf" Error

Hi all,

Recently I came across a "_scoreHalf" error in HMMSplicer for several, but not all, datasets. All my datasets are 100nt single end. The input fastq was generated from unaligned reads...
Forum: RNA Sequencing 03-10-2011, 04:52 AM
Replies: 29
Views: 12,481
Posted By proteomania
One quick question, does HMMSplicer identify...

One quick question, does HMMSplicer identify spliced reads spanning more than 1 junction?
Forum: RNA Sequencing 11-26-2010, 06:09 AM
Replies: 29
Views: 12,481
Posted By proteomania
Hi darked89, Yes, you can use just the...

Hi darked89,

Yes, you can use just the unmapped reads. I have been doing this for a while, and the results of using unmapped reads and the full dataset are virtually the same. As far as I know,...
Forum: RNA Sequencing 11-24-2010, 10:51 AM
Replies: 29
Views: 12,481
Posted By proteomania
Thanks for developing the tool. The default...

Thanks for developing the tool. The default output doesn't seems to contain the alignmeant of the spliced reads, it would be great if the software could output the spliced read alignments in sam...
Forum: Bioinformatics 11-19-2010, 01:37 AM
Replies: 1
Views: 1,303
Posted By proteomania
Cufflinks merges adjacent genes

Hi all,

I am working on the RNA-Seq of an organism with very short intergenic distance (e.g. 50bp). I am using the TopHat/Cufflinks package for my analysis, and I found out Cufflinks tends...
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