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Forum: RNA Sequencing 08-23-2014, 06:46 AM
Replies: 2
Views: 3,490
Posted By sterding
I figured it out by using the...

I figured it out by using the "--compatible-hits-norm" option. See detail here:
https://www.biostars.org/p/86147/
Forum: Academic/Non-Profit Jobs 02-19-2014, 07:07 AM
Replies: 0
Views: 938
Posted By sterding
Computational Biologist in Brain Research @ Harvard Medical School

Harvard Medical School and Brigham & Women’s Hospital

Postdoctoral Position Available in The Neurogenomics Laboratory

Computational Biologist in Brain Research

The Neurogenomics Laboratory...
Forum: RNA Sequencing 11-11-2013, 08:55 AM
Replies: 2
Views: 3,490
Posted By sterding
Why does Cufflinks with mask (-M) option have lower FPKM for mRNA genes?

Dear all,

I was curious how much the -M (mask file) option can improve the FPKM from Cufflinks. From the mannual, it says

-M/--mask-file Tells Cufflinks to ignore all reads that could have come...
Forum: RNA Sequencing 11-08-2013, 01:02 PM
Replies: 13
Views: 8,465
Posted By sterding
hi Anelda, I made the genome.fa and gtf...

hi Anelda,

I made the genome.fa and gtf file in the same order, but still I got the " Segmentation fault" error in the step of " Learning bias parameters" if I use -b option. Without the "-b"...
Forum: RNA Sequencing 11-08-2013, 11:38 AM
Replies: 13
Views: 8,465
Posted By sterding
Thanks. I am testing this. I am also curious how...

Thanks. I am testing this. I am also curious how you found the trick :)
Forum: RNA Sequencing 11-08-2013, 10:30 AM
Replies: 3
Views: 2,534
Posted By sterding
Did you solve the problem? I have the same error...

Did you solve the problem? I have the same error as you, but occurring in the next step of "Inspecting reads and determining fragment length distribution."

I found another post...
Forum: Bioinformatics 08-23-2012, 12:52 PM
Replies: 0
Views: 1,165
Posted By sterding
How Tophat tell junctions from deletion?

HI,

I wrote to Cole for how Tophat tell the junctions (with CIGAR line xxxMxxxNxxxM) from deletions (xxxMxxxDxxxM). I guess they might be busy to answer all emails, so I dig the code myself a bit...
Forum: Bioinformatics 07-17-2012, 12:29 PM
Replies: 1
Views: 4,317
Posted By sterding
I made a learning note for SAM format, which...

I made a learning note for SAM format, which might be helpful to your question:

http://onetipperday.blogspot.com/2012/07/deeply-understanding-sam-tags.html
Forum: Bioinformatics 05-30-2012, 09:58 AM
Replies: 8
Views: 10,894
Posted By sterding
Thanks. I will try it.

Thanks. I will try it.
Forum: Bioinformatics 05-15-2012, 08:43 AM
Replies: 3
Views: 2,818
Posted By sterding
You are right; this option becomes user-settable...

You are right; this option becomes user-settable until the recent release.
Forum: Bioinformatics 05-10-2012, 01:02 PM
Replies: 8
Views: 10,894
Posted By sterding
Hi, Zheng. Is your question solved? or get...

Hi, Zheng.

Is your question solved? or get answered? I am also interested in the answer.

Best,

Xianjun
Forum: Bioinformatics 05-04-2012, 03:22 PM
Replies: 7
Views: 5,381
Posted By sterding
Anyone got clue to the question?

Anyone got clue to the question?
Forum: Bioinformatics 05-04-2012, 02:39 PM
Replies: 7
Views: 5,381
Posted By sterding
Here is the related text in the supplementary...

Here is the related text in the supplementary pdf:



But still, I am not clear how the p-value is calculated.
Forum: Bioinformatics 04-06-2012, 12:21 PM
Replies: 3
Views: 2,818
Posted By sterding
OK. Without any reply yet, I dig into the source...

OK. Without any reply yet, I dig into the source code of cufflinks by guessing something with threshold of 50. Yes, I did find some secret.

[sterding@hpcc01 cufflinks-1.3.0]$ grep -P "50\D" -I...
Forum: Bioinformatics 04-05-2012, 07:14 PM
Replies: 3
Views: 2,818
Posted By sterding
gap threshold in joining the reads in cufflinks?

I have a question to the de novo assembly using cufflinks: is there a threshold to join two non-overlapping reads?

As you can see from the attached figure, the top track is for alignment (BAM...
Forum: Bioinformatics 04-04-2012, 08:13 AM
Replies: 3
Views: 2,908
Posted By sterding
Here is the "call bowtie" part in tophat python...

Here is the "call bowtie" part in tophat python script. From what I can see (by a quick search), only -k, -m, -v (or -n) are set (see the red part below), which means only output the reads that have...
Forum: Bioinformatics 04-04-2012, 07:43 AM
Replies: 29
Views: 20,580
Posted By sterding
I just noticed that there are FLAG values of 256,...

I just noticed that there are FLAG values of 256, 272 (not just 0, 16, 4 for single-strand RNAseq). Since 256=256+0, 272=256+16, so we may assign 256 to plus (+) strand, and minus (-) for 272 reads. ...
Forum: Bioinformatics 04-03-2012, 08:46 PM
Replies: 29
Views: 20,580
Posted By sterding
Very useful post! I followed this post due...

Very useful post!

I followed this post due to the same problem: For strand-specific RNAseq data, the accepted_hits.sam (converted from BAM) from Tophat does not contain XS:A:+/- tag for unspliced...
Forum: Bioinformatics 04-03-2012, 02:17 PM
Replies: 14
Views: 19,443
Posted By sterding
Very useful! Thanks

Very useful! Thanks
Forum: Bioinformatics 02-17-2012, 11:17 AM
Replies: 1
Views: 5,557
Posted By sterding
This paper might be helpful: ...

This paper might be helpful:

http://www.nature.com/msb/journal/v7/n1/full/msb201128.html
Forum: Bioinformatics 01-12-2012, 08:42 AM
Replies: 4
Views: 4,045
Posted By sterding
This post helps a lot to the question here: ...

This post helps a lot to the question here:

http://biostar.stackexchange.com/questions/14122/changing-bowtie-settings-in-tophat
Forum: Illumina/Solexa 12-14-2011, 02:03 PM
Replies: 35
Views: 22,489
Posted By sterding
An IMPORTANT bug

Thanks for the code snip -- very nice!

I just found a bug in the code -- without chomp the newline character, the score will be wrong. Here is the new code:

cat fastq_file | perl -ne...
Forum: Bioinformatics 01-12-2011, 01:48 PM
Replies: 5
Views: 6,485
Posted By sterding
I simply extracted the record with keywords...

I simply extracted the record with keywords 'rRNA' or 'Mt' from hg19.gtf file by using command 'grep'.
Forum: Bioinformatics 12-08-2010, 02:46 PM
Replies: 5
Views: 6,485
Posted By sterding
I hope Cole have time for these questions :)

I hope Cole have time for these questions :)
Forum: Bioinformatics 12-08-2010, 10:36 AM
Replies: 10
Views: 13,951
Posted By sterding
Solved: It's a bug for OLD version of Tophat! Use version after v.1.1.3

Several things I think might be useful to share here:

1. For Illumina strand-unspecific single-end reads, when you used Tophat to map the reads, better NOT use the default option "--library-type...
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