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Search: Posts Made By: wenhuang
Forum: Bioinformatics 10-04-2011, 12:07 PM
Replies: 42
Views: 16,607
Posted By wenhuang
I think, that "intron chain" essentially means...

I think, that "intron chain" essentially means ignorance of the 5' end of the first exon and 3' end of the last exon. In other words, you get all the introns recovered, which does not necessarily...
Forum: Bioinformatics 09-28-2011, 07:18 AM
Replies: 4
Views: 5,145
Posted By wenhuang
what is a read group?

Hi,

I am sure this is a silly question, but what is a read group in bam files? A lane? a flow cell? a library? or any meaningful thing that can group reads together?

Thanks!

Wen
Forum: Bioinformatics 08-29-2011, 04:54 PM
Replies: 1
Views: 3,521
Posted By wenhuang
I think I have found the answer in this post ...

I think I have found the answer in this post

http://seqanswers.com/forums/showthread.php?t=12767

It turns out the alignment was at the end of the chromosome and contained a overhang which...
Forum: Bioinformatics 08-29-2011, 02:03 PM
Replies: 1
Views: 3,521
Posted By wenhuang
BWA output bitwise flag for mapped/unmapped reads

Hi everybody,

I have a question on a strange alignment I got with BWA (0.5.9). I have come up with a minimal test sequence



@5:84:16665:11131:Y...
Forum: Bioinformatics 11-20-2010, 09:39 PM
Replies: 1
Views: 4,015
Posted By wenhuang
UCSC -> Tables -> Choose the genome, group, and...

UCSC -> Tables -> Choose the genome, group, and track (Genes and e.g. RefSeq Genes) -> The trick is to set the output format to GTF.

Good luck.
Forum: Bioinformatics 11-09-2010, 07:29 PM
Replies: 5
Views: 2,426
Posted By wenhuang
Hi Adam, Glad to see this post brought your...

Hi Adam,

Glad to see this post brought your attention :).

I used Tophat 1.1.1 and Cufflinks 0.9.2.

Mine is paired end reads. I don't see XS tags for unspliced reads but I see XS tags with...
Forum: RNA Sequencing 11-08-2010, 06:00 PM
Replies: 9
Views: 9,458
Posted By wenhuang
I think both Cufflinks and Scripture can do...

I think both Cufflinks and Scripture can do single end data, at least their strategy (very similar) to stitch alignments together does not seem to need paired end data. Of course, paired end data...
Forum: RNA Sequencing 11-08-2010, 02:54 PM
Replies: 9
Views: 9,458
Posted By wenhuang
I don't think intronic read fraction depends on...

I don't think intronic read fraction depends on annotation, unless you count "intergenic" reads as intronic.

I did a highly simplified calculation to see the effect of pre-mRNA fraction.
...
Forum: Bioinformatics 10-20-2010, 08:24 AM
Replies: 9
Views: 10,109
Posted By wenhuang
pileup in samtools may be what you need.

pileup in samtools may be what you need.
Forum: Bioinformatics 10-18-2010, 05:23 PM
Replies: 5
Views: 2,426
Posted By wenhuang
cufflinks "x" class code

Hi,

In the newest version of cufflinks, there is a "x" class code documented as "exonic overlap with reference on the opposite strand".

I have encountered many assembled single-exon...
Forum: Bioinformatics 08-23-2010, 09:33 AM
Replies: 0
Views: 1,369
Posted By wenhuang
RNA-seq alignment to closely related genome

Hi,

I have recently done alignment of an RNA-seq library for an organism (bos indicus cattle, the zebu cattle) without reference genome to a closely related genome (bos taurus cattle). The mapped...
Forum: Bioinformatics 07-01-2010, 12:00 PM
Replies: 1
Views: 2,002
Posted By wenhuang
Scripture output

Hi,

Does anybody know what is the fifth column in a Scriputure (http://www.broadinstitute.org/software/scripture/) bed output for?

The documentation says Scripture also outputs RPKM, and this...
Forum: RNA Sequencing 06-17-2010, 07:15 AM
Replies: 9
Views: 9,458
Posted By wenhuang
I am not sure it is so dependent on annotation. ...

I am not sure it is so dependent on annotation.

The 30% intronic reads I got was the fraction of reads mapped to known genes, not total mapped reads. If you have a less complete annotation, exonic...
Forum: RNA Sequencing 06-16-2010, 06:17 PM
Replies: 9
Views: 9,458
Posted By wenhuang
I have limited amount of RNA ~10ng, so I...

I have limited amount of RNA ~10ng, so I amplified it using Ambion's MessageAmp and sequenced the aRNA by a 75x2 GA run.

I read somewhere on this forum that intron retention is more than frequent,...
Forum: Bioinformatics 06-15-2010, 09:18 PM
Replies: 1
Views: 1,876
Posted By wenhuang
rna-seq read distribution

I first posted the following thread at the RNA-seq sub forum. I found this place is much more popular :)

Hi,

I wonder how reads mapped to the genome (contiguously or to junctions) are...
Forum: RNA Sequencing 06-15-2010, 07:49 AM
Replies: 7
Views: 6,348
Posted By wenhuang
I have used messageAmp from Ambion for...

I have used messageAmp from Ambion for amplification and was able to get sequencing to work, sort of...

One problem I have is reads are severely biased towards the 3'end. So recovery of full...
Forum: RNA Sequencing 06-15-2010, 07:46 AM
Replies: 9
Views: 9,458
Posted By wenhuang
RNA-seq read distribution

Hi,

I wonder how reads mapped to the genome (contiguously or to junctions) are distributed.

My own experience has surprisingly high fraction mapped to introns (over 30% of reads mapped to known...
Forum: Bioinformatics 05-20-2010, 09:36 AM
Replies: 6
Views: 4,610
Posted By wenhuang
polyA containing reads in RNA-seq

Hi,

I am just curious if any of the existing softwares for RNA-seq analysis handles polyA containing reads. I am not aware of one that explicitly tries to map polyA containing reads.

Thanks!
Forum: Bioinformatics 04-22-2010, 05:37 PM
Replies: 2
Views: 6,113
Posted By wenhuang
I had the same question before and it was...

I had the same question before and it was answered by Cole Trapnell in this thread:
http://seqanswers.com/forums/showthread.php?t=4355

basically you can specify a negative integer. My results...
Forum: Bioinformatics 04-21-2010, 08:04 AM
Replies: 0
Views: 2,320
Posted By wenhuang
cufflinks class code

Hi,

Does anybody know the rules cufflinks used to determine the class codes of assembled transcripts? For example, how transcripts from the same locus are bundled? Is "c" reciprocal (assembled...
Forum: Bioinformatics 04-19-2010, 11:40 AM
Replies: 46
Views: 29,736
Posted By wenhuang
Hi Simon, Thank you for your work....

Hi Simon,

Thank you for your work. Unfortunately, although I am able to get the yeast data provided on your website to work with htseq-count, I am not able to get my own data to work. The SAM file...
Forum: Bioinformatics 04-18-2010, 10:11 AM
Replies: 46
Views: 29,736
Posted By wenhuang
Hi Simon, Thanks for your reply. I ended up...

Hi Simon,

Thanks for your reply. I ended up using tophat and it has no problem aligning overlapping reads by specifying a negative -r as suggested by Cole Trapnell.

I attached an example SAM...
Forum: Bioinformatics 04-17-2010, 06:10 PM
Replies: 46
Views: 29,736
Posted By wenhuang
Hi Simon, Can I ask you a question that if I...

Hi Simon,

Can I ask you a question that if I have paired end reads who are overlapping with each other, for a overlapped region, does HTSeq count it as single coverages if reads are from the same...
Forum: Bioinformatics 04-10-2010, 09:22 AM
Replies: 3
Views: 2,645
Posted By wenhuang
I found out that there were not many cases like...

I found out that there were not many cases like this.

I ended up filtering based on the bitwise flag in the second column of the SAM file simply using awk. Paired end reads mapping to different...
Forum: Bioinformatics 04-09-2010, 09:50 AM
Replies: 3
Views: 2,645
Posted By wenhuang
tophat paired reads mapped to different chromosomes

Hi,

I noticed that tophat some times can map paired end reads to different chromosomes (see one example below). The sequences are undoubtedly of low complexity.

I haven't looked to see how...
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