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Search: Posts Made By: christinawu2008
Forum: Bioinformatics 02-19-2014, 02:35 PM
Replies: 3
Views: 672
Posted By christinawu2008
I have the problem, Can I please know how you...

I have the problem, Can I please know how you ended up?
Forum: Bioinformatics 12-04-2013, 02:07 PM
Replies: 5
Views: 1,760
Posted By christinawu2008
Thanks gringer So seems to need some...

Thanks gringer

So seems to need some additional scaffolding steps from other programs...

Regards,
Chen
Forum: Bioinformatics 12-01-2013, 01:14 PM
Replies: 5
Views: 1,760
Posted By christinawu2008
Hi there, I think so, but there is no 'N's...

Hi there,

I think so, but there is no 'N's in the output assembly, which were generated from SOAP-trans.. which makes me think Trinity discards the transcripts containing Ns after doing...
Forum: Bioinformatics 06-07-2013, 04:00 AM
Replies: 2
Views: 787
Posted By christinawu2008
Thanks. I haven't employed mate pairs. It's right...

Thanks. I haven't employed mate pairs. It's right that the gaps are sometimes estimated large because the insert size of pairs are normally following a distribution, which we just set a constant...
Forum: Bioinformatics 06-04-2013, 07:15 PM
Replies: 2
Views: 787
Posted By christinawu2008
GapCloser from SOAP

Hi, I just tried GapCloser from SOAP and it seems breaking some scaffolds down which causes a decrease of N50 length... what happens? :confused:

It indeed closes a large part of gaps (Ns from...
Forum: Bioinformatics 05-21-2013, 02:22 PM
Replies: 20
Views: 6,709
Posted By christinawu2008
So I guess from the tricky way, read 2 should be...

So I guess from the tricky way, read 2 should be trimmed using 'a' first and then '-g'?

I have the data with junction adapter shorter than the read length, so it can present anywhere or overlap to...
Forum: Bioinformatics 05-24-2012, 05:52 PM
Replies: 1
Views: 439
Posted By christinawu2008
quality management

Hi All,

I want to ask if I do different trimming for different datasets (some kept 50bp, some are with 80bp left). does it influence DE analysis? :confused:

Christina
Forum: Bioinformatics 06-28-2011, 10:07 PM
Replies: 205
Views: 47,389
Posted By christinawu2008
problem with SSPACE

Hi

I have a problem of using SSPACE. the process was failed at bowtie-build. I can use bowtie to do index with my genome file, but it seems not working in SSPACE... What's the problem?

Thanks
Forum: Bioinformatics 06-28-2011, 07:25 PM
Replies: 16
Views: 3,393
Posted By christinawu2008
bowtie-build error

Hi boetsie,

SSPACE must be very useful tool for scaffolding. But when I tried to use it, the process was failed by bowtie-build step. I only have contig file contains all name with super_contig...
Forum: RNA Sequencing 05-01-2011, 10:48 PM
Replies: 20
Views: 4,925
Posted By christinawu2008
Hi Simon, Can you post out the literatures...

Hi Simon,

Can you post out the literatures related to comparing GE between using microarray and RNA-Seq, and prove your views? Even though I agree with you, but I'd like to see some published...
Forum: RNA Sequencing 05-01-2011, 10:06 PM
Replies: 20
Views: 4,925
Posted By christinawu2008
May be some artefacts in your data and you can...

May be some artefacts in your data and you can detect them by comparing replicates and discard them.
Forum: Illumina/Solexa 05-01-2011, 08:51 PM
Replies: 4
Views: 1,169
Posted By christinawu2008
Hi suludana, Thank you! Are there any...

Hi suludana,

Thank you!

Are there any literatures described how large is the expected read output (Gbases) for each sample in illumina RNA-Seq? (mammalian) if the genome is 3Gbases.
Forum: Illumina/Solexa 04-27-2011, 11:54 PM
Replies: 4
Views: 1,169
Posted By christinawu2008
Unhappy questions about choosing read coverage

Hi everyone,

It sounds stupid question... but I really want to know how you guys choose the read coverage before sequencing. I know it is related to the cost. But What is the minimum size and what...
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