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Search: Posts Made By: arrchi
Forum: Bioinformatics 06-10-2013, 07:03 AM
Replies: 1
Views: 2,030
Posted By arrchi
problems with running Cufflinks using Gencode annotation gtf

Hi there,

Has anybody successfully run Cufflinks with human RNA-Seq data set using Gencode annotation gtf?

I've been trying to run commands like this "cufflinks --num-threads 4 -g...
Forum: Bioinformatics 04-05-2013, 12:59 PM
Replies: 3
Views: 1,098
Posted By arrchi
Thanks a lot for all your suggestions. FastQC per...

Thanks a lot for all your suggestions. FastQC per base sequence quality plot shows the last base of second reads is missing. I agree, the Ns only happen at the end of the second read, it won't make a...
Forum: Bioinformatics 04-05-2013, 12:17 PM
Replies: 3
Views: 1,098
Posted By arrchi
unknown bases in a RNA-Seq data

Hi there,

I just got a RNA-Seq 50bp paired-end data generated by Illumina HiSeq. A strange thing is all the last base of the paired reads are N. For example:

$ head -4 m1.R1.fastq...
Forum: Bioinformatics 02-07-2013, 10:00 AM
Replies: 13
Views: 3,237
Posted By arrchi
Thanks a lot, jb2.

Thanks a lot, jb2.
Forum: Bioinformatics 02-07-2013, 09:03 AM
Replies: 13
Views: 3,237
Posted By arrchi
yes, the 36,497,412 is the total number of my raw...

yes, the 36,497,412 is the total number of my raw reads.
Forum: Bioinformatics 02-07-2013, 07:40 AM
Replies: 13
Views: 3,237
Posted By arrchi
tophat bam shows more reads than the library

Hi there,

I've run tophat (version 2.0.4 and encode gtf) to a paired-end 50bp RNA-Seq data . The fastq files shows the total number of reads is 36,497,412, after tophat run, I used samtools to...
Forum: Bioinformatics 09-04-2012, 09:51 AM
Replies: 1
Views: 1,210
Posted By arrchi
update

I re-installed tophat (v 2.0.4) and the problem is fixed :)
Forum: Bioinformatics 09-04-2012, 05:30 AM
Replies: 1
Views: 1,210
Posted By arrchi
tophat warning and files in /tmp are not cleared

Hi there,

I ran tophat on human 50-bp PE reads generated by HiSeq 2000, it seems it finished because all files should be generated by tophat were generated (such as bam and bed files), but the...
Forum: Bioinformatics 08-30-2012, 10:22 AM
Replies: 2
Views: 1,735
Posted By arrchi
fastQC output question

Hi there,

Here is one of the reports from fastQC. In the per_base_quality plot, the first 11 bases look weird. I wonder if I need to trim the first 11 bases? And possible reasons?

Thank a bunch.
Forum: Bioinformatics 08-29-2012, 07:44 AM
Replies: 2
Views: 2,793
Posted By arrchi
agree

eager to know if there is any new development.
Forum: Bioinformatics 08-29-2012, 05:40 AM
Replies: 0
Views: 2,647
Posted By arrchi
tophat2 warning?

Hi there,

I am running tophat on a RNA-seq data set containg PE 50-bp reads from Illumina HiSeq. The number of reads for each sample is about 85 million. I got a warning "couldn't remove all...
Forum: Bioinformatics 01-13-2012, 12:51 PM
Replies: 12
Views: 3,789
Posted By arrchi
found some helpful information here in case one...

found some helpful information here in case one is wondering this type of question like me:http://seqanswers.com/forums/showthread.php?t=4349
Forum: Bioinformatics 01-13-2012, 12:29 PM
Replies: 8
Views: 5,724
Posted By arrchi
Can edgeR/DESeq have more than one covariate?

Beside diagnosis, can I include age, gender and etc as covariates in the GLM model? I could not find such information in their paper or manual.

Thanks a lot.
Forum: Bioinformatics 01-13-2012, 12:22 PM
Replies: 12
Views: 3,789
Posted By arrchi
Is it a reason that we can not fit a GLM model...

Is it a reason that we can not fit a GLM model with FPKM value directly since FPKM is a probability?
Forum: Bioinformatics 01-13-2012, 11:39 AM
Replies: 12
Views: 3,789
Posted By arrchi
I found cpm in their source package.

I found cpm in their source package.
Forum: Bioinformatics 01-13-2012, 11:22 AM
Replies: 12
Views: 3,789
Posted By arrchi
Thanks for all responses. That's right....

Thanks for all responses.

That's right. Cufflink-cuffcompare-cuffdiff gives results of paired samples, but not between two conditions.

I am reading the paper and the manual of "edgeR", you...
Forum: Bioinformatics 01-13-2012, 09:25 AM
Replies: 12
Views: 3,789
Posted By arrchi
As far as I understand, DESeq and EdgeR identify...

As far as I understand, DESeq and EdgeR identify differentiated genes, but not transcripts/isoforms. I wish they have extended their software's ability to isoform level.
Forum: Bioinformatics 01-13-2012, 07:08 AM
Replies: 12
Views: 3,789
Posted By arrchi
differentiated expression analysis on isoforms/transcripts level

Hi there,

I have a RNA-seq data (3 cases and 4 controls). I am looking for ways to identify differentiated isoforms/transcripts in these two conditions. Any suggestions besides t-test?

Thanks.
Forum: Bioinformatics 12-06-2011, 01:20 PM
Replies: 16
Views: 11,680
Posted By arrchi
Thanks again. I think these sequences (CGTCTG and...

Thanks again. I think these sequences (CGTCTG and TATCTCGTATG) will be removed if i do adapter trimming?

Do you have experience of using any software to trim adapter sequence?
Forum: Bioinformatics 12-06-2011, 12:05 PM
Replies: 16
Views: 11,680
Posted By arrchi
Great. Thanks. But the k-mer plot shows peaks at...

Great. Thanks. But the k-mer plot shows peaks at the right side instead of left side.

Did you know how to derive the adapter sequence? I thought an adapter from Illumina is 12 fixed 6-bp...
Forum: Bioinformatics 12-06-2011, 11:10 AM
Replies: 16
Views: 11,680
Posted By arrchi
Thanks, mgg. Sorry, I think I did not...

Thanks, mgg.

Sorry, I think I did not describe my question clearly.

The 57% is from fastQC "Overrepresented sequences" section. The first two rows look like this:



Column 3 just says the...
Forum: Bioinformatics 12-06-2011, 07:44 AM
Replies: 16
Views: 11,680
Posted By arrchi
Hi mgg, How did you find this information...

Hi mgg,

How did you find this information from fastQC report "FastQC says 5.31% adapter"? Thanks.

At the meantime, I have a question for anybody. We have a human RNA seq data generated by...
Forum: Bioinformatics 11-30-2011, 08:01 AM
Replies: 1
Views: 2,382
Posted By arrchi
questions of illumina pe reads fastqc results

We have a set of illumina paired-end RNA seq 50 bp data. The plot of per base sequnece quality is fine (I think), but the plot of Kmer Content looks very weird. I want to have some suggestions about...
Forum: Bioinformatics 11-02-2011, 10:08 AM
Replies: 10
Views: 4,293
Posted By arrchi
Are you using human genome reference too? How...

Are you using human genome reference too? How many genes on chrM you got?
Forum: Bioinformatics 11-02-2011, 10:05 AM
Replies: 10
Views: 4,293
Posted By arrchi
Thanks for your reply. I used human genome...

Thanks for your reply. I used human genome reference. I repeated the same experiment but using an older version of cufflinks, I have genes on chrM.
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