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Search: Posts Made By: zslee
Forum: Bioinformatics 05-06-2014, 09:27 PM
Replies: 9
Views: 5,904
Posted By zslee
dexseq results understanding

Hey, Now I am trying to find splicing differences between two tumor and two normal samples(so only one condition: N and T factors), and prepare data following your vignette, everything goes well, but...
Forum: RNA Sequencing 12-20-2013, 01:31 AM
Replies: 1
Views: 1,768
Posted By zslee
Possible picard bug

Hey, I am running picard to remove pcr-duplicates using MarkDuplicates.jar
on bam file porduce by tophat(with fusion-serach on), and I encount:
Exception in thread "main"...
Forum: Bioinformatics 11-28-2013, 11:59 PM
Replies: 1
Views: 1,871
Posted By zslee
Defuse Calculating spanning p-values Failure

Hey, could anyone help me with one problem:
when I run defuse to find gene fusions based on fastq data (illumina HISEQ, paired-end, trimed by trimglore), the software goes well until Calculating...
Forum: Bioinformatics 07-21-2011, 04:20 AM
Replies: 4
Views: 3,382
Posted By zslee
OK, get it, thanks for the reply

OK, get it, thanks for the reply
Forum: Bioinformatics 07-19-2011, 01:07 AM
Replies: 4
Views: 3,382
Posted By zslee
no, I really just want part of the chromotogram...

no, I really just want part of the chromotogram trace, and screen capture is the one I did, but any other better methods?

thanks
Forum: Bioinformatics 07-18-2011, 06:02 AM
Replies: 4
Views: 3,382
Posted By zslee
asking about convert ab1 file to image

I have a sequencing chromotogram file in ab1 format, I can view it in softwares like chromatogram Explorer, but I want to show the chromatogram in my manuscript, so I need convert to a image file...
Forum: Bioinformatics 05-18-2010, 04:11 AM
Replies: 6
Views: 3,415
Posted By zslee
yes, just as you mentioned, i need mRNA not...

yes, just as you mentioned, i need mRNA not genomic sequences,
and in the paper i considered, they download data same as jiaco's suggestion
thanks to steven !
Forum: Bioinformatics 05-18-2010, 04:08 AM
Replies: 6
Views: 3,415
Posted By zslee
Red face yes, i've tried, it works, thanks to jiaco ! ...

yes, i've tried, it works, thanks to jiaco !
and i'm not familiar with UCSC
Forum: Bioinformatics 05-18-2010, 03:29 AM
Replies: 6
Views: 3,415
Posted By zslee
yes, i should make it clear ~

the paper i consider is
"Widespread RNA editing of embedded alu elements in the human transcriptome"
in the method part, they mentioned "We obtained all human and mouse full-length cDNA sequences...
Forum: Bioinformatics 05-18-2010, 12:00 AM
Replies: 6
Views: 3,415
Posted By zslee
about UCSC full length cDNA

in one paper, they use downloaded full length cDNA sequences(from ucsc) to detect A-to-I rna editing by aligning to reference hg16, but when i want to repeat their work by downloading human mRNA...
Forum: Bioinformatics 03-04-2010, 12:29 AM
Replies: 11
Views: 3,292
Posted By zslee
Smile OK, thanks a lot ! i understand now

OK, thanks a lot ! i understand now
Forum: Bioinformatics 03-04-2010, 12:21 AM
Replies: 11
Views: 3,292
Posted By zslee
something i don't understand of samtools pileup result

chr10 856918 A W 109 109 60 15 ,...T,..t.,T,,, aaN`a_aa`_`_b__
the above is one line of my samtool pileup results, in this position, the reference base is A, so the...
Forum: Bioinformatics 02-15-2010, 06:09 PM
Replies: 5
Views: 2,066
Posted By zslee
the reason is 3 different David gene id (that...

the reason is 3 different David gene id (that they used when do enrichment analysis) mapped to 1 ensemble gene id, the following is the answer from the David Guys:

Ensembl gene id was integrated...
Forum: Bioinformatics 02-09-2010, 04:58 PM
Replies: 5
Views: 2,066
Posted By zslee
i 've checked that, this gene id exist only once...

i 've checked that, this gene id exist only once in both my test gene list and background
i don't know the resason yet ...
Forum: Bioinformatics 02-08-2010, 06:15 AM
Replies: 5
Views: 2,066
Posted By zslee
about David, why one gene is calculated 3 times ?

have anyone used David to do function enrichment analysis on line ?
i have got one line like bellow:

Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold...
Forum: Bioinformatics 01-21-2010, 04:43 AM
Replies: 0
Views: 1,673
Posted By zslee
has anyone analyses GLFv3 format?

samtools can Generate genotype likelihood in the binary GLFv3 format, i want ot analyses the genotype data, but which tools can be used to analyses this GLFv3 output ?

thanks in advance
Forum: Illumina/Solexa 01-15-2010, 05:04 PM
Replies: 2
Views: 1,497
Posted By zslee
OK,thanks for you reply and sorry for my english...

OK,thanks for you reply and sorry for my english :(
i understand ~~
Forum: Illumina/Solexa 01-14-2010, 10:02 PM
Replies: 2
Views: 1,497
Posted By zslee
how high-through sequencing detect I? as G ?

i am doing rna editing analysis using solexa data,
i wann know which base is a I detected as ? even though it's translated as G in vivo
thanks
Forum: Bioinformatics 01-09-2010, 05:03 AM
Replies: 2
Views: 1,640
Posted By zslee
yes, that's maybe what i 'll do if no other...

yes, that's maybe what i 'll do if no other better tools
Forum: Bioinformatics 01-07-2010, 03:50 AM
Replies: 2
Views: 1,640
Posted By zslee
how to get snps

hello guys.
i have hundreds of locations on the human genome, and i wish to check whether they're snps and what is the minor base, is there some better way than to downlaod them all and write code...
Forum: Bioinformatics 12-13-2009, 10:31 PM
Replies: 2
Views: 3,426
Posted By zslee
samtools -pileup can produce base mapping and...

samtools -pileup can produce base mapping and mutation information, does this help you ?
Forum: Bioinformatics 12-10-2009, 04:56 PM
Replies: 8
Views: 2,634
Posted By zslee
thanks to you all i 'll first use krobison's...

thanks to you all
i 'll first use krobison's suggestion and consider sift later
~~
Forum: Bioinformatics 12-08-2009, 04:54 PM
Replies: 8
Views: 2,634
Posted By zslee
SIFT (Sorting Intolerant From Tolerant) is a...

SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function
my work is simpler, i just want to know whether a change of bases on...
Forum: Bioinformatics 12-07-2009, 11:37 PM
Replies: 8
Views: 2,634
Posted By zslee
to decide whether a mutation is non-synonimous or not

i have short solexa sequences mapping to genome, in some positions there're
some certain enriched mutations, how do i know whether this mutation is non-synonimous or not ?
one method is download...
Forum: Bioinformatics 11-25-2009, 12:08 AM
Replies: 3
Views: 3,555
Posted By zslee
as for splicing sites, i think at least in...

as for splicing sites, i think at least in protein coding genes it should be exact the exon-intron boundary, because any error may cause frame shift.
i think you want to know the length of sequence...
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