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Forum: Bioinformatics 04-13-2014, 01:07 AM
Replies: 1
Views: 1,009
Posted By weasteam
Hi vinaydu, The example of miRPara results...

Hi vinaydu,

The example of miRPara results can be find at https://code.google.com/p/mirpara/wiki/miRPara

Please scroll down to bottom and feel free to let me know if you have more questions.
Forum: Bioinformatics 05-10-2013, 10:15 AM
Replies: 2
Views: 2,519
Posted By weasteam
Thank you kokonech, I will compare the result...

Thank you kokonech, I will compare the result outputed from htseq-count and easyrnaseq.
Forum: Bioinformatics 05-08-2013, 07:16 AM
Replies: 2
Views: 2,519
Posted By weasteam
how does stranded and un-stranded quantification work?

I have one stranded library and it was aligned to genome in both un-stranded (--library-type fr-unstranded) and stranded (--library-type fr-firststrand) methods (with tophat). The gene level counts...
Forum: Bioinformatics 05-03-2013, 07:26 AM
Replies: 0
Views: 1,423
Posted By weasteam
Solution for easyRNASeq RPKM value = NA

I was having problems in generate the rpkm values from easyRNASeq, everything I got is "NA".

The problem is because the easyRNASeq could not calculate the total reads from one bam file. The...
Forum: Bioinformatics 05-02-2013, 02:28 PM
Replies: 0
Views: 1,008
Posted By weasteam
Solution for easyRNASeq Error in .doBasicCount(obj)

If you are using easyRNASeq and if you see the following error

Error in .doBasicCount(obj) : The genomicAnnotation slot is empty

This is because the chromosome name from annotation file is...
Forum: Bioinformatics 05-02-2013, 10:38 AM
Replies: 3
Views: 1,594
Posted By weasteam
Awesome paper, thank you for sharing.

Awesome paper, thank you for sharing.
Forum: Bioinformatics 05-01-2013, 07:36 AM
Replies: 3
Views: 1,594
Posted By weasteam
List of RNA-Seq bioinformatics tools

Just want to share the page I just found, it seems like no one have ever shared this one before:

http://en.wikipedia.org/wiki/List_of_RNA-Seq_bioinformatics_tools
Forum: Bioinformatics 11-24-2012, 12:34 PM
Replies: 0
Views: 865
Posted By weasteam
miRPara 6.1 Released

Hi,

Thank you for using miRPara.

The new miRPara (version 6.1) is released. The major updates includes
1) replacing Algorithm::SVM with libsvm. Algorithm::SVM has not been updated since 2008...
Forum: Bioinformatics 08-20-2012, 08:22 PM
Replies: 0
Views: 984
Posted By weasteam
miRPara4.2 Released

http://159.226.126.177/mirpara/title.jpg
miRPara4.2 is just released.

Updates:

fixed bug [uninitialized value $loop in lc at miRPara.pl line 813.]
optimized the UNAFold.pl & ct2out...
Forum: General 08-19-2012, 03:22 PM
Replies: 11
Views: 3,368
Posted By weasteam
Sorry, I did not notice your reply. please...

Sorry, I did not notice your reply. please download the most updated miRPara, miRPara4.2 at http://www.whiov.ac.cn/bioinformatics/mirpara or http://code.google.com/p/mirpara/downloads/list, it should...
Forum: Bioinformatics 06-29-2012, 06:39 AM
Replies: 0
Views: 1,566
Posted By weasteam
tophat trim options?

is there any way to add bowtie2 option "--trim5" or "--trim3" from tophat commend line?

Thanks.
Forum: General 06-08-2012, 06:38 AM
Replies: 11
Views: 3,368
Posted By weasteam
Do you mind sent the sequence to me? I can debug...

Do you mind sent the sequence to me? I can debug the miRPara and solve the problem for you.
Forum: General 06-07-2012, 02:43 PM
Replies: 11
Views: 3,368
Posted By weasteam
hi, have you installed ct2out? if yes, did you...

hi, have you installed ct2out? if yes, did you copy this file to the /usr/local/bin/?
Forum: Bioinformatics 02-16-2012, 11:13 AM
Replies: 9
Views: 7,488
Posted By weasteam
here you go: http://www.oceanridgebio.com/ ...

here you go:
http://www.oceanridgebio.com/

#!/usr/bin/perl
# by Yonggan Wu
# yongganw@oceanridgebio.com
# Ocean Ridge Bioscience LLC
# Version 01 Date: 2012-02-16 15:01:08
# Version 01...
Forum: Bioinformatics 02-16-2012, 08:23 AM
Replies: 2
Views: 1,763
Posted By weasteam
did you use the bam file generated from tophat? ...

did you use the bam file generated from tophat?

I have the same problem if I use a bam file from CASAVA, but not from tophat.
Forum: Bioinformatics 02-16-2012, 08:21 AM
Replies: 2
Views: 1,430
Posted By weasteam
have same problem here, still wondering why...

have same problem here,

still wondering why cuffdiff does not utilize multiple threads after mapping...too slow...

I tried to split the gtf files, and it was not working well.
Forum: Bioinformatics 02-03-2012, 01:21 PM
Replies: 4
Views: 10,113
Posted By weasteam
How to filter FASTQ Quality?

FASTX can do FASTQ Quality Filter (http://hannonlab.cshl.edu/fastx_toolkit/commandline.html),

[-q N] = Minimum quality score to keep.
[-p N] = Minimum percent of bases that must have...
Forum: Bioinformatics 01-03-2012, 11:18 AM
Replies: 2
Views: 2,342
Posted By weasteam
Thanks GenoMax, the fastq files are...

Thanks GenoMax,

the fastq files are demultiplexed, it should be ready to go.

I am contacting the company to hand me the full "Unaligned" folder. Hopefully, I am able to run it tomorrow.
Forum: Bioinformatics 01-02-2012, 02:23 PM
Replies: 2
Views: 2,342
Posted By weasteam
How to do CASAVA alignment by using fastq files

Hi, I am trying to make CASAVA1.8 work.

The company give me the demultiplexing data (in fastq format), Can some one please let me know how to do the alignment with CASAVA1.8?

I am very confused...
Forum: Illumina/Solexa 01-02-2012, 08:58 AM
Replies: 24
Views: 9,394
Posted By weasteam
I installed the Ubuntu in my Mac, it works very...

I installed the Ubuntu in my Mac, it works very well.
Forum: Illumina/Solexa 12-23-2011, 01:10 PM
Replies: 8
Views: 5,524
Posted By weasteam
Ho yeah, I am back with solutions: In linux,...

Ho yeah, I am back with solutions:

In linux, try following two lines in termnal:

sudo ln -s /usr/lib/x86_64_linux_gun/lib2.so /usr/lib
sudo ln -s /usr/lib/x86_64_linux_gun/libpth* /usr/lib
Forum: General 11-11-2011, 08:34 AM
Replies: 11
Views: 3,368
Posted By weasteam
Yes, this is better, I can predict for whole...

Yes, this is better, I can predict for whole viruses geneomes.
Forum: General 06-15-2011, 12:32 AM
Replies: 11
Views: 3,368
Posted By weasteam
Really? I randomly selected one sequence from...

Really?
I randomly selected one sequence from mirbase and it works.
>rno-mir-216a MI0000955...
Forum: General 06-05-2011, 05:34 PM
Replies: 11
Views: 3,368
Posted By weasteam
yes, let me know if you have any questions.

yes, let me know if you have any questions.
Forum: Illumina/Solexa 02-03-2009, 02:53 AM
Replies: 2
Views: 2,748
Posted By weasteam
hi, xuer, thank you for your replay. Since I have...

hi, xuer, thank you for your replay. Since I have not get any data about my project, I guess no one would know it. I just want to take a view of other's data which might be similar to mine, with...
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