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Forum: Bioinformatics 10-10-2019, 04:29 AM
Replies: 1
Views: 1,697
Posted By rajarapupriya
Hope you solved your problem. But for anyone who...

Hope you solved your problem. But for anyone who is having the same problem, use lapply function in R to convert any integers to numeric. This solved my problem. Here is the code I used...
Forum: Bioinformatics 01-16-2019, 10:25 AM
Replies: 1
Views: 548
Posted By rajarapupriya
Hi, I guess that the number of transcripts for...

Hi,
I guess that the number of transcripts for that particular bacteria are more that they could cover 98% of their respective genome. If you do not expect this maybe you need to change the binning...
Forum: RNA Sequencing 10-05-2018, 08:55 AM
Replies: 0
Views: 1,009
Posted By rajarapupriya
Error while extracting fasta seqeunces from stringtie merged gtf.

I have used stringtie -merge option to get a merged gtf file of my assembly. However, when I use gffread to extract sequences from the merged gtf, I get the following error.

Error (GFaSeqGet):...
Forum: RNA Sequencing 10-05-2018, 07:50 AM
Replies: 2
Views: 2,467
Posted By rajarapupriya
Hi, I ran into the same error recently....

Hi, I ran into the same error recently. Fortunately was able to fix. My gtf file looks the same, however the genome fasta had extra information in the name. For example, your fasta file should also...
Forum: Bioinformatics 06-01-2018, 10:09 AM
Replies: 62
Views: 27,236
Posted By rajarapupriya
Thanks for your quick reply. I ran a test run...

Thanks for your quick reply. I ran a test run with both the references in the same command.
Forum: Bioinformatics 06-01-2018, 09:05 AM
Replies: 62
Views: 27,236
Posted By rajarapupriya
Hi Brain, Thanks for developing great tools...

Hi Brain,

Thanks for developing great tools for the community :) !!
We are using bbsplit to separate insect and it's symbiont transcripts from a ribodepleted transcriptome. However, the reference...
Forum: RNA Sequencing 09-11-2014, 10:48 AM
Replies: 1
Views: 1,625
Posted By rajarapupriya
Hi Sindrle, Can you please give more details...

Hi Sindrle,

Can you please give more details on how you measured the protein and also what are you referring to as a "wired thing" in the picture that you attached.

Priya
Forum: RNA Sequencing 03-28-2014, 07:21 AM
Replies: 6
Views: 3,744
Posted By rajarapupriya
Thank you, Jeremy !!

Thank you, Jeremy !!
Forum: RNA Sequencing 03-27-2014, 12:59 PM
Replies: 6
Views: 3,744
Posted By rajarapupriya
Thanks, Michael !! Think I missed it somewhere. ...

Thanks, Michael !! Think I missed it somewhere.

Priya
Forum: RNA Sequencing 03-27-2014, 07:36 AM
Replies: 6
Views: 3,744
Posted By rajarapupriya
Thanks Jeremy for replying to my question. I...

Thanks Jeremy for replying to my question. I would like to change FDR before/while calculating the differential gene expression. I'm using DESeq2 1.2.10 Vignette. The entire differential expression...
Forum: RNA Sequencing 03-24-2014, 12:06 PM
Replies: 6
Views: 3,744
Posted By rajarapupriya
Changing FDR in DESeq2

Could anyone please tell me how to change the FDR from default (0.1) to 0.05 in DESeq2.

Thanks
Priya
Forum: Bioinformatics 03-20-2014, 05:05 AM
Replies: 6
Views: 1,937
Posted By rajarapupriya
Awesome !! I appreciate your efforts !! ...

Awesome !! I appreciate your efforts !!

Thanks again
Priya
Forum: Bioinformatics 03-19-2014, 05:40 AM
Replies: 6
Views: 1,937
Posted By rajarapupriya
Dear Wolfgang, I am trying to use DESeq2 as...

Dear Wolfgang,

I am trying to use DESeq2 as I have seen many changes from the previous version. I am having a lot of trouble following the data (raw read counts) input part.
In the vignette it...
Forum: RNA Sequencing 01-17-2014, 07:41 AM
Replies: 14
Views: 7,992
Posted By rajarapupriya
Yayy !! It worked. I was giving the wrong order...

Yayy !! It worked. I was giving the wrong order of dataframe and input file in cds command line. Thanks a lot for your time Devon !!
Priya
Forum: RNA Sequencing 01-17-2014, 07:34 AM
Replies: 14
Views: 7,992
Posted By rajarapupriya
Hi Devon, > is.numeric(rownames(counts)) ...

Hi Devon,

> is.numeric(rownames(counts))
[1] FALSE
> is.numeric(colnames(counts))
[1] FALSE
Here is the output for the command. I guess, my dataframe is right as my first row and column have...
Forum: RNA Sequencing 01-17-2014, 07:28 AM
Replies: 14
Views: 7,992
Posted By rajarapupriya
Hi Devon, Thanks for your quick reply. But, just...

Hi Devon, Thanks for your quick reply. But, just wondering if the command is "is.numeric()"
Forum: RNA Sequencing 01-17-2014, 07:12 AM
Replies: 14
Views: 7,992
Posted By rajarapupriya
I have the same issue and I've also worked...

I have the same issue and I've also worked previously with DESeq. I checked if my text file has any empty rows or columns, but of no use. Any suggestions would be greatly appreciated.
Thanks
Forum: Introductions 10-29-2013, 09:47 AM
Replies: 0
Views: 1,098
Posted By rajarapupriya
Smile Introduction

Hello,

All set to know more about NGS !!

:)
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