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Search: Posts Made By: muthu545
Forum: RNA Sequencing 04-08-2016, 07:07 AM
Replies: 4
Views: 1,698
Posted By muthu545
Hi, The best easy solution is to export the...

Hi,

The best easy solution is to export the results to excel and do an inverse of log2FC column.

Note: Tweaking cuffdiff object is bit tedious.
Forum: Ion Torrent 08-25-2014, 03:00 PM
Replies: 12
Views: 8,705
Posted By muthu545
Chayan, The script only allows you to extract...

Chayan,
The script only allows you to extract Fastq sequences by length and not by quality.
Hopefully you would have figures that out by now. sorry for the late reply.

Thanks
--
Muthu
Forum: Ion Torrent 12-14-2013, 06:12 AM
Replies: 12
Views: 8,705
Posted By muthu545
Hi Wing, Devon's solution for the problem is...

Hi Wing,

Devon's solution for the problem is right. Thanks.
The script errored out, as it was not able to recognize the
outfile file.



Thanks
--
Forum: Bioinformatics 07-05-2013, 12:37 PM
Replies: 10
Views: 7,578
Posted By muthu545
Kelsey, Rightnow, its throwing out error...

Kelsey,

Rightnow, its throwing out error because its not able to detect the directory 'DIRPATH' and the gtf file.

I mentioned 'DIRPATH' in order to imply the directory in which you have the...
Forum: Bioinformatics 07-05-2013, 12:31 PM
Replies: 10
Views: 7,578
Posted By muthu545
Hi Kelsey, Not a problem. If that's the...

Hi Kelsey,

Not a problem.

If that's the case (Galaxy's output is .tabular), then you could rename the files in order to change the .tabular file format, after you download them.

If R cannot...
Forum: Bioinformatics 07-03-2013, 03:07 PM
Replies: 10
Views: 7,578
Posted By muthu545
Kelsey, As Sazz mentioned, the output files...

Kelsey,

As Sazz mentioned, the output files from cuffdiff will not have .tabular file formats.
Please verify your output files from cuffdiff, if it doesnot match names provided in the...
Forum: Bioinformatics 07-03-2013, 02:11 PM
Replies: 14
Views: 7,139
Posted By muthu545
Areyes and Zimmernv, Could you let me know,...

Areyes and Zimmernv,

Could you let me know, how could I get flattened GTF file with 'real' exons instead of the exonic parts?

Thanks
--
Muthu
Forum: Bioinformatics 07-03-2013, 02:08 PM
Replies: 10
Views: 7,578
Posted By muthu545
Hi kelseyca, cuffData.db is the database...

Hi kelseyca,

cuffData.db is the database file created by cummeRbund to store all the results from cuffdiff in a easy to access format for commands in cummeRbund in R.

So if you run...
Forum: RNA Sequencing 06-28-2013, 06:34 AM
Replies: 3
Views: 1,812
Posted By muthu545
Thank you, Simon.

Thank you, Simon.
Forum: RNA Sequencing 06-27-2013, 11:17 AM
Replies: 3
Views: 1,812
Posted By muthu545
HTSeq to DESeq

Hi all,

HTSeq's count file output contains # of reads for
no_feature
ambiguous
too_low_aQual
not_aligned
alignment_not_unique

I used to delete them from my gene matrix before inputting...
Forum: Bioinformatics 06-07-2013, 02:22 PM
Replies: 14
Views: 7,139
Posted By muthu545
Hi, I'm am novice to using DEXSeq. ...

Hi,

I'm am novice to using DEXSeq.
@zimmernv and @Alejandro
How could you get the flattened GTF file with 'real' exons instead of the exonic parts?

Thanks
--
Muthu
Forum: Bioinformatics 05-30-2013, 07:01 AM
Replies: 2
Views: 2,832
Posted By muthu545
Hi, The Code suggested by GenoMax is very...

Hi,

The Code suggested by GenoMax is very useful. I'm just providing a modification of the code:

Store the SRR096001-SRR096999 #s that would want to download in a file:
for example:
cat >...
Forum: Bioinformatics 05-29-2013, 08:55 AM
Replies: 11
Views: 3,100
Posted By muthu545
Hi, If the issue is only on the # of files,...

Hi,
If the issue is only on the # of files, you could try combining batches of 100 files - which will leave you with 130 combined files (13000/100) ---> then you could combine these 130 files to 1...
Forum: Bioinformatics 05-28-2013, 03:46 PM
Replies: 11
Views: 3,100
Posted By muthu545
Sure, once you have the head and tail of 3...

Sure, once you have the head and tail of 3 Files... We could figure out some code that could concatenate all your 13000 files into one.

Thanks
--
Muthu
Forum: Bioinformatics 05-28-2013, 03:34 PM
Replies: 11
Views: 3,100
Posted By muthu545
If I understand it right, what you want to get...

If I understand it right, what you want to get to....
Input:
File 1: 0 - 1000
File 2: 0 - 1000

Output:
File 0 -2000

For this you must all the end coordinate of file1 to all of File 2...
Forum: Bioinformatics 05-28-2013, 03:18 PM
Replies: 11
Views: 3,100
Posted By muthu545
Just a Suggestion... You could use cat function...

Just a Suggestion...
You could use cat function and then do sorting [sort function] on the coordinates to put them in order.

Thanks
--
Forum: Bioinformatics 05-28-2013, 01:06 PM
Replies: 5
Views: 2,594
Posted By muthu545
Hi, I think you could try local fit, if it...

Hi,

I think you could try local fit, if it does not throw out error.

Are you using DESeq1.X version or DESeq2.X

Thanks
--
Muthu
Forum: Bioinformatics 05-28-2013, 12:29 PM
Replies: 5
Views: 2,594
Posted By muthu545
Hi, plotDispEst plots the dispersion vs...

Hi,
plotDispEst plots the dispersion vs rowCounts of DESeq object.
Usually as shown in the Vignette, the dispersions will be higher with lower row counts and go on to decrease with increasing row...
Forum: Bioinformatics 05-28-2013, 11:57 AM
Replies: 10
Views: 1,705
Posted By muthu545
Hi Phillie, The actual figure in the print...

Hi Phillie,

The actual figure in the print should look like the following
http://alamo.uthscsa.edu/webfolder/BLAST%20explanation.jpg

The # in red color are the right numbers.

Hope this...
Forum: Bioinformatics 05-28-2013, 11:30 AM
Replies: 10
Views: 1,705
Posted By muthu545
I agree with you, philie.... Some of the values...

I agree with you, philie.... Some of the values are wrong in the figure.
As you mentioned in your first post the value for E-->L cell should be -2.
I updated my previous post.


Thanks
--...
Forum: Bioinformatics 05-28-2013, 10:59 AM
Replies: 3
Views: 3,986
Posted By muthu545
GATK is open source...

GATK is open source...
Forum: Bioinformatics 05-28-2013, 10:32 AM
Replies: 10
Views: 1,705
Posted By muthu545
Hi Philie, Sorry the making it more...

Hi Philie,

Sorry the making it more confused for you,
As you mentioned some of the values in the figure presented in the links are wrong

Imagine its a 2X2 matrix
-->E L
P -3 -4
E ...
Forum: Bioinformatics 05-28-2013, 10:00 AM
Replies: 10
Views: 1,705
Posted By muthu545
Hi Sorry I had my labelings for upper, left...

Hi
Sorry I had my labelings for upper, left and upper-left interchanged and confused you
First computation is [Upper-left] P ---> E = -3 + -1 (for mismatch) = -4
Second computation is [Upper]...
Forum: Bioinformatics 05-28-2013, 08:44 AM
Replies: 10
Views: 1,705
Posted By muthu545
Hi, I looked at the matrix, the value of -0...

Hi,

I looked at the matrix, the value of -0 for L and E comparison is right.
As per their explanation, you have to perform 3 computations.
First computation is [Upper] P ---> E = -3 + -1 (for...
Forum: Bioinformatics 05-28-2013, 07:12 AM
Replies: 3
Views: 2,322
Posted By muthu545
Hi, For Read counts data set matrix (35000...

Hi,

For Read counts data set matrix (35000 genes * 20 samples),
First filter all the genes that is zero across all the samples.

Second, load the filtered dataset in R using DESeq package -->...
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