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Forum: Bioinformatics 07-18-2012, 05:17 AM
Replies: 4
Views: 4,627
Posted By jlli
You can try cutadapt :...

You can try

cutadapt : http://code.google.com/p/cutadapt/
or
fastx clipper : http://hannonlab.cshl.edu/fastx_toolkit/index.html

Tha cutadapt has more options.
Forum: Academic/Non-Profit Jobs 01-04-2011, 05:41 PM
Replies: 0
Views: 1,498
Posted By jlli
Bioinformatics Scientist at Sanford-Burnham Orlando

The Sanford-Burnham Medical Research Institute at Lake Nona, Florida is seeking a full-time Bioinformatics scientist to analyze sequences and numerical data produced by a variety of genome-scale...
Forum: SOLiD 03-30-2010, 05:13 AM
Replies: 6
Views: 2,986
Posted By jlli
(24.0.0): The first number is the number of...

(24.0.0): The first number is the number of color bases of the read are matched to the reference. In this case is 24; the second number is number of mismathces; and the third one is offsets. In...
Forum: SOLiD 12-10-2009, 08:16 AM
Replies: 26
Views: 14,258
Posted By jlli
We just got the Bioscope, it would be great if...

We just got the Bioscope, it would be great if you can share the results of bfast vs. bioscope.
Forum: SOLiD 07-06-2009, 07:13 AM
Replies: 13
Views: 4,893
Posted By jlli
Thanks for the replies, these really clear up my...

Thanks for the replies, these really clear up my confusion. In my study, I only want to map the reads to reference genome so far. I used same criteria as westerman (2 for 25bp, 3 for 35bp, 6 for...
Forum: SOLiD 06-30-2009, 06:09 AM
Replies: 13
Views: 4,893
Posted By jlli
How to set mismatches?

For SOLiD color-space mapping, we usually allow 2 mismatches for 25bp, 3 mismatches for 35bp. With SOLiD v3, the read length goes to 50bp. What is the max mismatches for 50bp. How about 75bp? And...
Forum: SOLiD 05-28-2009, 06:24 PM
Replies: 1
Views: 1,933
Posted By jlli
I used N. The corona-lite only accepts the A,...

I used N. The corona-lite only accepts the A, C, T, G, and N.
Forum: SOLiD 04-30-2009, 07:11 AM
Replies: 4
Views: 3,273
Posted By jlli
Many thanks, I got it.

Many thanks, I got it.
Forum: SOLiD 04-29-2009, 06:30 PM
Replies: 4
Views: 3,273
Posted By jlli
I agree that we need to aviod immediately jumping...

I agree that we need to aviod immediately jumping to base space for alignment. Here here is what I am concerning.

For example, I have reference sequence
Base space: TCGAGCAGCACGTC
color...
Forum: SOLiD 04-29-2009, 05:43 AM
Replies: 4
Views: 3,273
Posted By jlli
colorspace mapping

If I do not work with SNP detection, can I just translate the colorspace to basespace, then do the mapping? One thing concerning me is that a single mismatch in colorspace not only affects the...
Forum: SOLiD 02-13-2009, 06:59 AM
Replies: 10
Views: 2,968
Posted By jlli
although MAQ is not truly designed to work with...

although MAQ is not truly designed to work with SOLiD data, so functions have been added to convert solid reads to fastq
Forum: SOLiD 02-12-2009, 06:13 PM
Replies: 10
Views: 2,968
Posted By jlli
How about MAQ?

How about MAQ?
Forum: SOLiD 01-13-2009, 09:20 AM
Replies: 24
Views: 7,768
Posted By jlli
corona-lite

corona-lite
Forum: Genomic Resequencing 01-13-2009, 08:16 AM
Replies: 14
Views: 10,678
Posted By jlli
PLoS ONE. 2008;3(12):e4012. Epub 2008 Dec 24. ...

PLoS ONE. 2008;3(12):e4012. Epub 2008 Dec 24.
Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing.
Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I.
...
Forum: SOLiD 01-13-2009, 05:39 AM
Replies: 24
Views: 7,768
Posted By jlli
For human genome and 50G reads, it tooks about...

For human genome and 50G reads, it tooks about 36 hours for mapping (1 cpu, 6G memory).
Forum: SOLiD 11-21-2008, 05:37 PM
Replies: 14
Views: 4,433
Posted By jlli
SOLiD ma2gff

Does anyone have experience with SOLiD GFF Conversion Tool (ma2gff)? I downloaded MaToGffSRC.0.2.04.zip from SOLiD software web site, but it is difficult to install it into unix.

Many thanks,
Forum: Bioinformatics 10-05-2008, 07:55 PM
Replies: 27
Views: 10,480
Posted By jlli
ElandtoBed.jar at FindPeak package...

ElandtoBed.jar at FindPeak package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Forum: Illumina/Solexa 08-07-2008, 05:46 PM
Replies: 6
Views: 3,762
Posted By jlli
Does SOLiD sequencing generate these artificial...

Does SOLiD sequencing generate these artificial repetitive reads near the edge of a slide? We observed similar behavior from our SOLiD ChIPSeq project. We have no clue where went wrong.
Forum: Bioinformatics 08-06-2008, 06:54 AM
Replies: 0
Views: 3,182
Posted By jlli
An HMM approach to genome-wide identification of differential histone modification si

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.
Xu H, Wei CL, Lin F, Sung WK.
...
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