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Forum: Bioinformatics 11-03-2013, 03:07 AM
Replies: 1
Views: 3,279
Posted By sqcrft
I got the same problem. not sure what is wrong....

I got the same problem. not sure what is wrong. One possible way is to do this:

seqlengths(x) = seqlengths(y)[names(seqlengths(x))]

force x to use the same seqlengths as y.
Forum: Academic/Non-Profit Jobs 10-26-2013, 11:53 PM
Replies: 1
Views: 1,473
Posted By sqcrft
Thank you for the information. It is probably...

Thank you for the information. It is probably better to ask in public for this information. What is the range of the salary for bioinformatics assistant professor in this University? Thank you very...
Forum: Epigenetics 08-18-2013, 03:45 AM
Replies: 0
Views: 2,536
Posted By sqcrft
MeRIPseq and m6A-seq data processing

If anyone is interested in RNA epigenetics or Post-transcriptional RNA modifications, we recently developed an R-package "exomePeak" for analysis of RNA epigenome sequencing data from MeRIPseq or...
Forum: RNA Sequencing 07-08-2013, 06:21 AM
Replies: 2
Views: 1,267
Posted By sqcrft
please share your code and what did you mean by...

please share your code and what did you mean by "doesn't work"?
Forum: Illumina/Solexa 03-11-2013, 08:44 AM
Replies: 4
Views: 2,288
Posted By sqcrft
thanks! That is really comforting. I had...

thanks! That is really comforting.
I had worried that the data and money might be wasted.
Forum: RNA Sequencing 03-11-2013, 07:53 AM
Replies: 8
Views: 2,410
Posted By sqcrft
Thanks, that is what I am doing now. I am using...

Thanks, that is what I am doing now.
I am using the ensembl gtf as reference, also split reads in to 2 piece of 20bp.

other option I am using is to set maximal intron size at 5kb to reduce false...
Forum: RNA Sequencing 03-11-2013, 06:42 AM
Replies: 8
Views: 2,410
Posted By sqcrft
I am now more inclined to use 20 x 2 now. But...

I am now more inclined to use 20 x 2 now. But probably I will try both, computation facility is free for me any way.

I can't find a source now to support the point: 3-piece is better, but I...
Forum: RNA Sequencing 03-11-2013, 06:15 AM
Replies: 8
Views: 2,410
Posted By sqcrft
Thanks, I will probably go with cufflinks later. ...

Thanks, I will probably go with cufflinks later.

but that is next step. right now the main issue to me is about the alignment.
The alignment needs to be optimized at the fist place before...
Forum: RNA Sequencing 03-11-2013, 06:10 AM
Replies: 8
Views: 2,410
Posted By sqcrft
thanks, that is what I am thinking. It seems to...

thanks, that is what I am thinking. It seems to me that tophat works better with 3 pieces, that is why they recommend a minimal 75 = 25 x 3 read length.

Now, I am not sure whether I should try cut...
Forum: Illumina/Solexa 03-11-2013, 05:33 AM
Replies: 4
Views: 2,288
Posted By sqcrft
Hi, fellow, is there any progress? I am stuck in...

Hi, fellow, is there any progress? I am stuck in the same dilemma.
The read length is too short, and we need to identify some novel transcripts.
Forum: RNA Sequencing 03-11-2013, 05:31 AM
Replies: 8
Views: 2,410
Posted By sqcrft
40bp paired reads for novel transcripts identification, which software?

I have some 40bp paired reads RNAseq data, basically that 40 x 2 from each RNA fragment.

It seems to me that, tophat prefers reads that is longer than 25. Is there some software that you recommend...
Forum: RNA Sequencing 01-10-2013, 07:05 AM
Replies: 7
Views: 5,606
Posted By sqcrft
I would suggest you to use p-value < 0.05. It is...

I would suggest you to use p-value < 0.05. It is not that statistically sound, but it should work.
Forum: RNA Sequencing 01-10-2013, 07:03 AM
Replies: 7
Views: 5,606
Posted By sqcrft
I have a number of experiments that have no DEGs...

I have a number of experiments that have no DEGs in cuffdiff result.
It seems to me that, cuffdiff v2 is too stringent.
Forum: Bioinformatics 12-12-2012, 07:54 AM
Replies: 3
Views: 3,231
Posted By sqcrft
I have the same problem, anybody has a clue?

I have the same problem, anybody has a clue?
Forum: Bioinformatics 11-29-2012, 05:06 AM
Replies: 5
Views: 8,094
Posted By sqcrft
check this:...

check this: http://user.list.galaxyproject.org/about-Mapping-Quality-td4366680.html

Jeremy,



This is not strictly correct. Tophat/bowtie don’t report mapping quality values that are as...
Forum: Bioinformatics 11-29-2012, 05:04 AM
Replies: 5
Views: 8,094
Posted By sqcrft
despite the sam format specification, 255 means...

despite the sam format specification, 255 means no mapq
Forum: Bioinformatics 11-29-2012, 05:04 AM
Replies: 5
Views: 8,094
Posted By sqcrft
some people say 255 means uniquely-mapped. but I...

some people say 255 means uniquely-mapped. but I can't find an source for that.
Forum: Bioinformatics 11-29-2012, 04:35 AM
Replies: 13
Views: 13,576
Posted By sqcrft
I don't think so. The option will report...

I don't think so.

The option will report only one mapping result out of all. It doesn't mean you get uniquely-mapped reads, you only get only one mapping result.

"If there are more alignments...
Forum: Bioinformatics 10-24-2012, 10:47 AM
Replies: 6
Views: 2,873
Posted By sqcrft
There is a tool that can convert the cufflinks...

There is a tool that can convert the cufflinks output gtf to the input of cpat bed format.
https://lists.soe.ucsc.edu/pipermail/genome/2011-April/025696.html

If you can integrate it into your...
Forum: Bioinformatics 10-23-2012, 08:25 AM
Replies: 6
Views: 2,873
Posted By sqcrft
my fault

Your bed format is the standard bed format.

Now, my only question will be how to combine cufflinks suite with your software to identify noval coding and non-coding transcripts.

It seems to be...
Forum: Bioinformatics 10-23-2012, 08:16 AM
Replies: 6
Views: 2,873
Posted By sqcrft
Thanks for your fast reply

Thanks for your fast reply.

Is there a direct way to connect PCAT with cufflinks/cuffmerge/cuffcompare?

As far as I can see, the 12 columns bed format required in your software has a different...
Forum: Bioinformatics 10-23-2012, 04:45 AM
Replies: 6
Views: 2,873
Posted By sqcrft
is it published?

the software is not published yet, right?
is there a paper?
Forum: Bioinformatics 08-03-2012, 04:24 AM
Replies: 21
Views: 4,642
Posted By sqcrft
Here is my experience, hope it may help a little...

Here is my experience, hope it may help a little bit.
The version 1.3 cuffdiff only give FPKM of a condition, but not the FPKMs of individual replicates. I realized that some condition FPKMs from...
Forum: Bioinformatics 08-02-2012, 04:13 AM
Replies: 21
Views: 4,642
Posted By sqcrft
Are you using different gene annotation gtf files...

Are you using different gene annotation gtf files in cuffdiff and cufflinks?
combined.gtf and cuffcmp.combined.gtf
Forum: Bioinformatics 08-01-2012, 04:03 AM
Replies: 21
Views: 4,642
Posted By sqcrft
I meant, the version 2.02 cuffdiff also output...

I meant, the version 2.02 cuffdiff also output the FPKM of all the replicates, so there is no need to run the cufflinks anymore.
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