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Search: Posts Made By: jason_ARGONAUTE
Forum: Bioinformatics 11-05-2013, 08:51 PM
Replies: 1
Views: 1,339
Posted By jason_ARGONAUTE
Question DESeq NB test for samples without biological replicates

Hi guys,

I hv encountered problems performing negative binomial test for samples without replicates while control group has replicates with DESeq.

Experimental design:
conduct the experiment...
Forum: Bioinformatics 11-05-2013, 12:15 AM
Replies: 2
Views: 4,849
Posted By jason_ARGONAUTE
perfect match with bowtie/bowtie2

Hi guys,

I have clean small RNA sequencing data at my hands. I wanna perform a perfect-match of miRNA to hairpin data from miRBase with Bowtie. However, i'm confused with its two mapping modes...
Forum: Bioinformatics 11-04-2013, 08:23 PM
Replies: 12
Views: 2,906
Posted By jason_ARGONAUTE
Wink many people told me to learn Python instead of...

many people told me to learn Python instead of Perl, maybe i'll learn python someday^^
Forum: Bioinformatics 11-04-2013, 08:19 PM
Replies: 12
Views: 2,906
Posted By jason_ARGONAUTE
i'm new to command awk, but thanks anyway^^

i'm new to command awk, but thanks anyway^^
Forum: Bioinformatics 11-04-2013, 08:18 PM
Replies: 12
Views: 2,906
Posted By jason_ARGONAUTE
i like the simplicity of linux commands, thank...

i like the simplicity of linux commands, thank you!
Forum: Bioinformatics 11-04-2013, 08:15 PM
Replies: 12
Views: 2,906
Posted By jason_ARGONAUTE
i like the simplicity, thank you!

i like the simplicity, thank you!
Forum: Bioinformatics 10-17-2013, 08:20 AM
Replies: 12
Views: 2,906
Posted By jason_ARGONAUTE
both of files are tab-delemited.

both of files are tab-delemited.
Forum: Bioinformatics 10-17-2013, 08:19 AM
Replies: 12
Views: 2,906
Posted By jason_ARGONAUTE
gene feature converter

Hi guys,
i hv got a GO file for my differentially expressed genes file, it goes like:

FBgn00001 GO:0016301 [Name:****(annotation)]
FBgn00002 GO:0016301 [Name:****(annotation)]
FBgn00003...
Forum: Bioinformatics 09-27-2013, 05:02 AM
Replies: 8
Views: 4,321
Posted By jason_ARGONAUTE
I hv tried htseq-count, really hard. But it...

I hv tried htseq-count, really hard.
But it cannt be installed on our lab server.
Thank you all the same^^
Forum: Bioinformatics 09-26-2013, 09:44 PM
Replies: 8
Views: 4,321
Posted By jason_ARGONAUTE
Or, what do i need to do to get raw counts for...

Or,
what do i need to do to get raw counts for each gene?
Thank you!
Forum: Bioinformatics 09-25-2013, 07:01 AM
Replies: 8
Views: 4,321
Posted By jason_ARGONAUTE
ya, i know and i do exactly as ur pipeline. might...

ya, i know and i do exactly as ur pipeline. might be i mixed the concept of exon and transcript. i thought they were the same thing.(both named "FBtrxxx")
So, this is not the reason why i got almost...
Forum: Bioinformatics 09-24-2013, 12:37 AM
Replies: 8
Views: 4,321
Posted By jason_ARGONAUTE
Dear swaraj, It helps me a lot....

Dear swaraj,

It helps me a lot. Thanks again^^
But i hv encountered a now problem now when adopting the new solution. I hv got 23017 exons in total while 14797 genes are mapped to...
Forum: Bioinformatics 09-23-2013, 06:51 AM
Replies: 8
Views: 4,321
Posted By jason_ARGONAUTE
thanks so much for ur script. But you didn't...

thanks so much for ur script.
But you didn't give the usage info.

I hv a .gtf file download from EMBL for D.mel now, should i convert it to .bed in advance?
and the usage is?
perl bed_count.pl ...
Forum: Bioinformatics 09-15-2013, 09:27 AM
Replies: 0
Views: 2,015
Posted By jason_ARGONAUTE
Question old release of mature miRNAs on miRBase (containing info abt dominant mature miR )

Data( latest release 20) on miRBase didn't tell which strain is the dominant one, it reports the sequence of both 3 prime and 5 prime miR. It contains 238 precusor miRNAs for Drosophila melanogaster....
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