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Forum: RNA Sequencing 05-24-2015, 01:46 AM
Replies: 0
Views: 865
Posted By fabrice
DEXSeq: How to get expresion value for each exon?

In my analysis, I do not want to compare exon based two conditions. I just want to get the expression value for each exon in each sample. How can I do it using DEXSeq?


dxd <-...
Forum: RNA Sequencing 05-22-2015, 07:30 PM
Replies: 1
Views: 1,087
Posted By fabrice
paper used HTSEQ and DEseq2

Dear all,

Where can I found some published paper which used HTSEQ and DEseq2 in their data analysis? Thank you very much in advance.
Forum: RNA Sequencing 05-22-2015, 07:25 PM
Replies: 192
Views: 54,415
Posted By fabrice
paper used HTSEQ and DEseq2

Dear all,

Where can I found some published paper which used HTSEQ and DEseq2 in their data analysis? Thank you very much in advance.
Forum: Bioinformatics 06-13-2014, 09:15 AM
Replies: 1
Views: 2,093
Posted By fabrice
Looking for tools for calling snv and indel(Somatic Variant)

Dear expert,
I am working on exome-seq data.
Looking for tools for calling snv and indel(Somatic Variant) in matched tumor-normal samples. Any suggestions?
Thank you very much in advance.
Forum: RNA Sequencing 02-07-2014, 12:04 PM
Replies: 2
Views: 1,319
Posted By fabrice
How to get gene symbol after deseq?

Dear experts,

After I have run deseq, I got a list of genes. They are something like as follow.

> resSig[,1]
[1] "ENSMUSG00000022150+ENSMUSG00000079102:009" ...
Forum: RNA Sequencing 11-04-2013, 06:00 AM
Replies: 1
Views: 1,170
Posted By fabrice
cat tophat.log [2013-11-01 17:39:45]...

cat tophat.log

[2013-11-01 17:39:45] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2013-11-01 17:39:45] Checking for Bowtie
Bowtie version: 2.1.0.0...
Forum: RNA Sequencing 11-04-2013, 05:59 AM
Replies: 1
Views: 1,170
Posted By fabrice
Tophat 2.0.9 only output chr1-7 in junctions.bed

The log file segment_juncs.log

segment_juncs v2.0.9 (4112M)
---------------------------
[samopen] SAM header is present: 84 sequences.
Loading reference sequences...
Loading chr1...done...
Forum: Bioinformatics 07-18-2013, 05:29 AM
Replies: 1
Views: 1,103
Posted By fabrice
Is there any mature pipeline for DNA seq QC?

For example, coverage, read depth, read quality and map quality etc
Forum: Bioinformatics 04-08-2013, 12:31 PM
Replies: 74
Views: 35,722
Posted By fabrice
Thank you. I think it will be helpful. ...

Thank you.

I think it will be helpful.

I want to detect different splicing event in two different conditions. Have good suggestions?

Anyone try SplicingCompass:...
Forum: Bioinformatics 04-08-2013, 10:23 AM
Replies: 74
Views: 35,722
Posted By fabrice
Really lost. Too many tools.

Really lost. Too many tools.
Forum: RNA Sequencing 03-12-2013, 07:25 AM
Replies: 2
Views: 1,521
Posted By fabrice
14. SplitSeek It seems it is hot field.

14. SplitSeek

It seems it is hot field.
Forum: RNA Sequencing 03-11-2013, 01:52 PM
Replies: 2
Views: 1,521
Posted By fabrice
Software for splicing sites dectection using RNA-seq?

Dear expert,

Are there any software to detect splice sites/events using RNA-seq?

Thank you.

MATS:
http://rnaseq-mats.sourceforge.net/user_guide.htm

SpliceSeq
Forum: Bioinformatics 10-24-2012, 05:02 PM
Replies: 2
Views: 1,441
Posted By fabrice
swbarnes2, Thank you for your clarify. Yes....

swbarnes2,

Thank you for your clarify. Yes. I did not do a strand-specific library prepare. But I still have bit of problem to understand why I should expect to see reads in both directions.
The...
Forum: Bioinformatics 10-24-2012, 02:48 PM
Replies: 2
Views: 1,441
Posted By fabrice
Some confused from samtools mpileup.

When I run samtools with follow parameters:

samtools mpileup -C50 -Q25 -q1 -l %s -f %s %s

I got a output as follow:

21 34124586 G 38 ,,,,AAA,AAAAa..,,,aaa.AaA,,A,,aaaaaaaA

From...
Forum: Bioinformatics 11-05-2011, 03:54 AM
Replies: 2
Views: 2,978
Posted By fabrice
Why do you think that bwa doesn't actually use...

Why do you think that bwa doesn't actually use the base quality when mapping?
Forum: Bioinformatics 11-03-2011, 09:23 PM
Replies: 2
Views: 2,978
Posted By fabrice
GATK: Base quality score recalibration

Dear experts,

I have used GATK to Base quality score recalibration. After TableRecalibration, it will rewrite the quality scores (in the QUAL field) using the data in the recal_data.csv file, into...
Forum: RNA Sequencing 09-14-2011, 09:41 AM
Replies: 3
Views: 4,175
Posted By fabrice
Thank you.

Thank you.
Forum: RNA Sequencing 09-09-2011, 03:40 PM
Replies: 3
Views: 4,175
Posted By fabrice
novel isoform identification from RNA-seq

Is there any tools for this purpose?

Thanks.
Forum: Bioinformatics 08-23-2011, 01:21 AM
Replies: 1
Views: 1,350
Posted By fabrice
How to set a flag is mapped in sam/bam?

In sam/bam, there is flag which indicate this read is mapped/unmapped. I am wonder when this flag is set to mapped/unmapped? What is the criteria? If used different mapping tools, eg, bowtie, bwa,...
Forum: Bioinformatics 08-19-2011, 01:26 PM
Replies: 15
Views: 14,223
Posted By fabrice
Thanks. samtools is 0.1.17. I expect...

Thanks.

samtools is 0.1.17.

I expect that samtools flagstat will give bigger number than samtools view -F 4. But no, in my case.
Forum: Bioinformatics 08-19-2011, 12:50 PM
Replies: 15
Views: 14,223
Posted By fabrice
swbarnes2, Thank you for your reply. It...

swbarnes2,

Thank you for your reply.

It seems my question is not clear.

I used samtools view -F 4, which give a number how many reads are mapped.

Then I used samtools flagstat, it also...
Forum: Bioinformatics 08-19-2011, 12:25 PM
Replies: 15
Views: 14,223
Posted By fabrice
For pair-end data, samtools flagstat how to count?

For pair-end data, samtools flagstat how to count?
Forum: Bioinformatics 08-19-2011, 06:48 AM
Replies: 15
Views: 14,223
Posted By fabrice
kmcarr, Thank you. Yes. Now I can get the...

kmcarr,
Thank you.
Yes. Now I can get the mapped reads.
I do not understand why the reads number from "samtools view -F 4" is different to the "samtools flagstat" report mapped number.
The number...
Forum: Bioinformatics 08-19-2011, 05:01 AM
Replies: 0
Views: 1,414
Posted By fabrice
samtools flagstat and ViewSam ALIGNMENT_STATUS=Aligned

I am using and samtools flagstat to statistc how many reads mapped in my s_4.bam (produced by eland, convert from export files).

samtools flagstat s_4.bam

Then I used picard.

java -jar...
Forum: Bioinformatics 08-19-2011, 01:50 AM
Replies: 15
Views: 14,223
Posted By fabrice
It seems that there is not a flag to set which...

It seems that there is not a flag to set which reads mapped or not.
samtools view -f

6. In a string FLAG, each character represents one bit with
p=0x1 (paired), P=0x2 (properly paired),...
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