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Search: Posts Made By: louis7781x
Forum: Bioinformatics 07-09-2014, 01:42 AM
Replies: 4
Views: 1,439
Posted By louis7781x
Hi Senior Member thanks for your information...

Hi Senior Member

thanks for your information

I know that help screen show information of parameter

but I thinks it is a bit fuzzy, what is maximum mismatch allow in matched adapter or...
Forum: Bioinformatics 07-08-2014, 10:31 PM
Replies: 4
Views: 1,439
Posted By louis7781x
Hi Senior Member thanks for your information...

Hi Senior Member

thanks for your information

I know that help screen show information of parameter

but I thinks it is a bit fuzzy, what is maximum mismatch allow in matched adapter or ...
Forum: Bioinformatics 07-08-2014, 01:45 AM
Replies: 4
Views: 1,439
Posted By louis7781x
What is adapter trimming threshold of fastx_clipper?

Hi everyone

Does fastx_clipper have simple thread hold introduction, for example, minimum adapter match ? maximum mismatch allow? adapter sequence identity threshold?

I tried to find some...
Forum: Bioinformatics 11-28-2012, 01:27 AM
Replies: 0
Views: 1,475
Posted By louis7781x
The meaning of miRDeep2 score?

Hi ,does anyone know the mean of "miRDeep2 score" in report html file?

It is second column in report html file after running make_html.pl.

Thanks
Forum: Bioinformatics 04-15-2012, 06:17 AM
Replies: 1
Views: 1,517
Posted By louis7781x
An error about annotation exon number of gene in tophat-fusion report

I found an error about annotation gene.

In my result, one candidates report by tophat-fusion as follwing:

T2852 chr15-chr12 62173825 6979426 ff
6 1 6 2 35 41...
Forum: Bioinformatics 04-14-2012, 09:34 PM
Replies: 1
Views: 1,329
Posted By louis7781x
A command line for runing chimerascan

Hi

Does anyone had experience for using chimerascan.

I want to know the command line about chimerascan_html_table.py chimerascan_index.py chimerascan_run.py gtf_to_genepred.py ...
Forum: Bioinformatics 03-26-2012, 02:00 AM
Replies: 0
Views: 968
Posted By louis7781x
what is allowing error rate of bwa-sw ?

Does anyone know what is error rate(allow mismatch/indel with reference) of bwa-sw (default)?

I know error rate of bwa is < 3%.
Forum: Bioinformatics 03-20-2012, 12:36 AM
Replies: 2
Views: 3,243
Posted By louis7781x
First, It used discordant paired-end to find...

First,
It used discordant paired-end to find fusion candidates.
Example: |---geneA---|----------------------|---geneB---|

Second,
All unmapped reads from genome and exon-exon boundary will use...
Forum: Bioinformatics 12-12-2011, 07:20 AM
Replies: 5
Views: 3,397
Posted By louis7781x
Merge sai file of bwa ?

Hi everyone

I used bwa to align reads of multiple lane against genome,

Here I have a question.

For example,

If I have s_1_1_sequence.sai and s_1_2_sequence.sai and.. s_1_6_sequence.sai
Forum: Bioinformatics 12-04-2011, 05:51 AM
Replies: 2
Views: 3,111
Posted By louis7781x
Thanks a lot! I will install bx-python and...

Thanks a lot!

I will install bx-python and try the script again.
Forum: Bioinformatics 12-03-2011, 05:03 PM
Replies: 3
Views: 4,109
Posted By louis7781x
gene expression is equal to CDS of transcript....

gene expression is equal to CDS of transcript. You need to see information of each transcript of gene.
Forum: Bioinformatics 12-03-2011, 01:39 AM
Replies: 10
Views: 4,726
Posted By louis7781x
miRNA sequences obtained from release of miRBase...

miRNA sequences obtained from release of miRBase (release 8.2, July 2006)

It's long time no upadte.
Forum: Bioinformatics 12-03-2011, 12:44 AM
Replies: 2
Views: 3,111
Posted By louis7781x
Want to use extract_genomic_dna in command line

Hi everyone ,I want to use command line to run extract_genomic_dna.py from tool of galaxy.

Here is code of extract_genomic_dna.py.

In the beginning,need to import some module.

import sys,...
Forum: Bioinformatics 10-02-2011, 06:36 PM
Replies: 0
Views: 1,380
Posted By louis7781x
tophat how to detect indel ?

Does any one know tophat how to detect indel ?

Because tophat use bowtie to do alignment,but I know bowtie not allow indel so far .

Thanks!

Best Regard!
Forum: RNA Sequencing 08-22-2011, 02:56 AM
Replies: 3
Views: 2,807
Posted By louis7781x
Although there is no software to detect fusion...

Although there is no software to detect fusion gene in coloerspace now.

You can do as following,
First,using tophat to run your data .
Second,use function of FusionMap:--pereport to select...
Forum: Bioinformatics 08-15-2011, 05:21 AM
Replies: 0
Views: 1,714
Posted By louis7781x
[tophat-fusion]The priority of annotation is refGene or ensGene?‏

Hi,I have a question about annotation file of tophat-fusion.

The annotation file combined refGene and ensGene,my question is when location both annotated in refGene and ensGene,which is priority ?...
Forum: Bioinformatics 08-11-2011, 01:35 AM
Replies: 19
Views: 6,399
Posted By louis7781x
Supplying your own junctions: The options...

Supplying your own junctions:

The options below allow you validate your own junctions with your RNA-Seq data. Note that the chromosome names in the files provided with the options below must match...
Forum: Bioinformatics 08-11-2011, 01:26 AM
Replies: 19
Views: 6,399
Posted By louis7781x
You can see paper or ask them why that can detect...

You can see paper or ask them why that can detect splicing junction without annotation.


http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract...
Forum: Illumina/Solexa 08-10-2011, 11:21 PM
Replies: 1
Views: 3,838
Posted By louis7781x
Does ASCII 64 to 104 eq ASCII offset 33?

Hi,

I have illumina pipeline 1.3 RNA-seq paired-end data,I want to use bwa on galaxy.

The bwa on galaxy said it Must have Sanger-scaled quality values with ASCII offset 33 .

I know Illumina...
Forum: Bioinformatics 08-05-2011, 05:19 AM
Replies: 19
Views: 6,399
Posted By louis7781x
tophat with/without annotation,and cufflink with annotation?

Hi,

I want to know if I

(1)run tophat with annotation and use accepted_hits.bam to run cufflink with annotation

(2)run tophat without annotation and use accepted_hits.bam to run cufflink...
Forum: RNA Sequencing 08-05-2011, 05:14 AM
Replies: 0
Views: 1,362
Posted By louis7781x
Pick out high significant mutation from *.bed .

Hi,

I have used tophat to run rna-seq against to ref_genome without annotation,and it output indel discovery,insertion.bed and deletion.bed.

My question is how do I pick out high significant...
Forum: Bioinformatics 08-03-2011, 02:44 AM
Replies: 0
Views: 1,501
Posted By louis7781x
The problem of running soapfusion

Hi,I have a problem about running soapfusion.
After running soapfusion short(Alignment).I have alreay got result.out and result.2Seqs.

But when I ran perl soapfusion.pl(fusion discovery),I don't...
Forum: Bioinformatics 08-03-2011, 01:55 AM
Replies: 0
Views: 1,193
Posted By louis7781x
The problem of running soapfusion

Hi,I have a problem about running soapfusion.
After running soapfusion short(Alignment).I have alreay got result.out and result.2Seqs.

But when I ran perl soapfusion.pl(fusion discovery),I don't...
Forum: Literature Watch 08-03-2011, 01:11 AM
Replies: 11
Views: 6,221
Posted By louis7781x
Hi,I don't understand the column of result...

Hi,I don't understand the column of result output,UniqueCuttingPositionCount mean # of distinct reads. What is that mean?

I am confused with seed count.

Thanks !!
Forum: Illumina/Solexa 08-01-2011, 12:57 AM
Replies: 15
Views: 54,062
Posted By louis7781x
Hi,Does adapter also sequence too? I mean row...

Hi,Does adapter also sequence too? I mean row data has adapter sequence?
Showing results 1 to 25 of 74

 


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