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Forum: Illumina/Solexa 06-29-2011, 01:52 AM
Replies: 58
Views: 52,728
Posted By marcowanger
This is the error message I got from 0.5.1 p3

This is the error message I got from 0.5.1 p3
Forum: Illumina/Solexa 06-29-2011, 01:46 AM
Replies: 58
Views: 52,728
Posted By marcowanger
Dear Simon, I just downloaded 0.5.1.p3 . It...

Dear Simon, I just downloaded 0.5.1.p3 .

It seems there is no --stranded=reverse?




is it still a hidden function?
Forum: Illumina/Solexa 06-29-2011, 01:01 AM
Replies: 58
Views: 52,728
Posted By marcowanger
Dear Simon, How can I modify the code...

Dear Simon,

How can I modify the code to reverse the --strand from counting coding strand to template strand?
Forum: Illumina/Solexa 06-16-2011, 09:57 PM
Replies: 58
Views: 52,728
Posted By marcowanger
Talking It make more sense. We used dUTP so we got...

It make more sense. We used dUTP so we got template strand.
Forum: Illumina/Solexa 06-10-2011, 09:25 PM
Replies: 58
Views: 52,728
Posted By marcowanger
Flobpf, nice to hear from you again. May you...

Flobpf, nice to hear from you again.

May you kindly do some illustration? I got the protocol from our sequencing center and it seems the other way round. Maybe we have different protocol?
...
Forum: Illumina/Solexa 03-22-2011, 02:18 AM
Replies: 58
Views: 52,728
Posted By marcowanger
Thanks Simon.

Thanks Simon.
Forum: Illumina/Solexa 03-17-2011, 08:07 PM
Replies: 58
Views: 52,728
Posted By marcowanger
As Simon assumes. Then it probably explains...

As Simon assumes.

Then it probably explains why I got extremely low count for nearly all of the genes.
Forum: Illumina/Solexa 03-17-2011, 08:01 PM
Replies: 58
Views: 52,728
Posted By marcowanger
To strengthen our understanding on this issue,...

To strengthen our understanding on this issue, perhaps we should take a look at the paper on strand specific sequencing.

I take this for an example....
Forum: Illumina/Solexa 03-17-2011, 05:34 AM
Replies: 58
Views: 52,728
Posted By marcowanger
I think this "thread" should be moved to...

I think this "thread" should be moved to "bioinformatics"?
Forum: Illumina/Solexa 03-17-2011, 05:16 AM
Replies: 58
Views: 52,728
Posted By marcowanger
Maybe first we have to clarify the terms so that...

Maybe first we have to clarify the terms so that we can discuss on the same line.

Please correct me if I am wrong,

Strandness in GTF/GFF file: Strand of the gene, the coding strand of the RNA,...
Forum: Illumina/Solexa 03-17-2011, 05:09 AM
Replies: 58
Views: 52,728
Posted By marcowanger
In fact I just used BWA to illustrate the...

In fact I just used BWA to illustrate the scenario. I faced the problem using tophat BAM.....
Forum: Illumina/Solexa 03-17-2011, 05:07 AM
Replies: 58
Views: 52,728
Posted By marcowanger
flobpf, I think that is 2 different issues we are...

flobpf, I think that is 2 different issues we are talking about here.

The term "strandness" puzzled me so much.

Strandness of the read:
The second column is about the strandness of the read's...
Forum: Illumina/Solexa 03-16-2011, 10:15 PM
Replies: 58
Views: 52,728
Posted By marcowanger
I mean in the meantime, I should 1> 2>...

I mean in the meantime, I should

1>
2> Filter the tagged sam by Htseq -o, filter the reads mapped to the gene that are tagged by Tophat XS:A:[+/-] with the strand matching the Gene strand in...
Forum: Illumina/Solexa 03-16-2011, 08:39 PM
Replies: 58
Views: 52,728
Posted By marcowanger
Thanks flobpf

Thanks flobpf
Forum: Illumina/Solexa 03-16-2011, 08:34 PM
Replies: 58
Views: 52,728
Posted By marcowanger
One thing come into my mind. We used strand...

One thing come into my mind.

We used strand specific (ss) paired-end sequencing.

And from illumina's website, the ss prep only works on single read flow cell only

And Simon you mentioned
Forum: Illumina/Solexa 03-16-2011, 07:57 PM
Replies: 58
Views: 52,728
Posted By marcowanger
The protocol we used 1> Poly-A selection,...

The protocol we used

1> Poly-A selection, Fragmentation
2> First strand cDNA synthesis
3> Second strand syntehsis with dUNTP
4> end repair,3' end A-tailing, Adapter ligation (i have no idea if...
Forum: Illumina/Solexa 03-16-2011, 07:50 PM
Replies: 58
Views: 52,728
Posted By marcowanger
Thanks for the clarification. Would you mind...

Thanks for the clarification.

Would you mind help me explain the following observation?

I used htseq-count -t exon -i Name --mode=union --stranded=[yes/no] -o input.tagged.sam...
Forum: Illumina/Solexa 03-16-2011, 06:42 AM
Replies: 58
Views: 52,728
Posted By marcowanger
I am a bit confused. According to Simon Anders ...

I am a bit confused. According to Simon Anders



I assume htseq count the read that map to the sense/antisense according the the strand of feature, so we should use --stranded=yes?

But...
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