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Search: Posts Made By: reema
Forum: Bioinformatics 06-09-2015, 02:56 PM
Replies: 0
Views: 1,090
Posted By reema
Testing a force topology in mrBayes

Hello Everybody,


I have a question related to "Testing a topological hypothesis". I have
tried to run the same procedure as mentioned in the tutorial in order to
check whether two species form...
Forum: Bioinformatics 06-02-2015, 08:23 AM
Replies: 1
Views: 995
Posted By reema
CEGMA complete/partial depend on number of sequences?

Hello Everybody

I have a question related to CEGMA complete and partial score . We have done the assembly by Trinity and then assembled trinity transcripts in more complete transcript set. Now...
Forum: Bioinformatics 04-01-2015, 02:54 AM
Replies: 2
Views: 1,371
Posted By reema
See :-...

See :- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3493127/
https://www.biostars.org/p/77756/
http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/
Forum: Bioinformatics 03-24-2015, 07:37 AM
Replies: 4
Views: 4,527
Posted By reema
Hello diego, Here the solution...

Hello diego,

Here the solution http://sourceforge.net/p/htseq/bugs/12/
Forum: Bioinformatics 03-17-2015, 07:18 AM
Replies: 2
Views: 1,784
Posted By reema
Hello xunong Hypergeometric distribution is...

Hello xunong

Hypergeometric distribution is used in case of microarray data.
Are you using RNAseq data? If yes- then i would suggest to use GOseq R package. You can create your own GO instance...
Forum: Bioinformatics 03-06-2015, 08:23 AM
Replies: 1
Views: 1,466
Posted By reema
Problem solved. For solution please see...

Problem solved. For solution please see https://www.biostars.org/p/133348/
Forum: Bioinformatics 03-04-2015, 09:47 AM
Replies: 1
Views: 1,466
Posted By reema
De-novo assembly PASA annotation

Hello Everyone,

We have recently generated two de-novo transcriptomics assembly for two different but related species. These new transcripts seem quite good on the basis of quality measurements,...
Forum: Bioinformatics 09-24-2014, 01:07 AM
Replies: 3
Views: 7,127
Posted By reema
Please see...

Please see https://blast.ncbi.nlm.nih.gov/BLAST_guide.pdf. Especially page number 9 and question 4.9.
I hope this helps.

Thanks,
Reema
Forum: Bioinformatics 09-22-2014, 08:10 AM
Replies: 3
Views: 7,127
Posted By reema
But in order to find distant related sequences I...

But in order to find distant related sequences I used Psi-blast. Here the link http://www.protocol-online.org/biology-forums/posts/26387.html
Forum: Bioinformatics 09-22-2014, 08:04 AM
Replies: 1
Views: 2,249
Posted By reema
Hello, Please see this link :-...

Hello,

Please see this link :- http://seqanswers.com/forums/showthread.php?t=46711. Well I was also very much confused about singleton. As rick mentioned in this post that align reads without...
Forum: Bioinformatics 09-22-2014, 07:54 AM
Replies: 4
Views: 7,061
Posted By reema
Thanks Rick, This is really helpful :) Reema...

Thanks Rick, This is really helpful :)

Reema Singh,
Forum: Bioinformatics 09-18-2014, 02:43 AM
Replies: 4
Views: 7,061
Posted By reema
Hi Rick, Thanks for explaining this so...

Hi Rick,

Thanks for explaining this so clearly. It means When we align reads back to the new assembly, and in the alignment summary reads having only one pair e.g only left pair align and only...
Forum: Bioinformatics 09-17-2014, 03:09 AM
Replies: 4
Views: 7,061
Posted By reema
What is Singletons?

Dear Friends,

I would like to ask :- What is Singletons especially in a de-novo transcriptomics assembly? I known this sound silly:), but I am really very eager to known the exact information...
Forum: Bioinformatics 09-15-2014, 01:19 AM
Replies: 7
Views: 3,379
Posted By reema
Thanks kbradnam for explaining this so clearly...

Thanks kbradnam for explaining this so clearly and nicely. I understand now :)

Many Thanks,
Reema Singh
Forum: Bioinformatics 09-12-2014, 07:47 AM
Replies: 7
Views: 3,379
Posted By reema
Hello kbradnam Thanks for sharing the link....

Hello kbradnam

Thanks for sharing the link. But i have one more quick question.

partial score is higher than complete score from both assembly(generated from two different samples). As far as...
Forum: Bioinformatics 09-11-2014, 07:02 AM
Replies: 7
Views: 3,379
Posted By reema
Hello peromhc and kbradnam, Thank you very...

Hello peromhc and kbradnam,

Thank you very much for your reply. Sorry for getting back late- As I first want to run cegma on my assembly before posting the reply. Here's the update:-

1) CEGMA...
Forum: Bioinformatics 08-31-2014, 01:30 PM
Replies: 7
Views: 3,379
Posted By reema
CEGMA - FATAL ERROR when running local map 6400

Hello Everyone,

I am trying to get the CEGMA score for our new transcriptome assembly. But when I tried to run cegma on my assemled transcripts, I am getting following error:-

"RUNNING:...
Forum: Bioinformatics 03-05-2014, 07:27 AM
Replies: 2
Views: 2,150
Posted By reema
Thanks TiborNagy, You are right,my file is...

Thanks TiborNagy,

You are right,my file is not paired.:(.
Forum: Bioinformatics 02-27-2014, 03:03 AM
Replies: 11
Views: 2,591
Posted By reema
How about using logFold change?

How about using logFold change?
Forum: Bioinformatics 02-27-2014, 02:59 AM
Replies: 2
Views: 2,150
Posted By reema
Talking Picard SamToFastq strange behavious

Dear all,

I am using picard SamtoFastq in oredr to convert BAM/SAM to fastq. I have a paired end sample. I am using following command:-

java -jar SamToFastq.jar INPUT=input.bam...
Forum: Bioinformatics 02-27-2014, 02:49 AM
Replies: 2
Views: 2,388
Posted By reema
Thanks yueluo,

Thanks yueluo,
Forum: Bioinformatics 02-13-2014, 08:37 AM
Replies: 6
Views: 2,011
Posted By reema
Smile Thanks, Now I posted as a new thread.:)

Thanks,

Now I posted as a new thread.:)
Forum: Bioinformatics 02-13-2014, 08:36 AM
Replies: 2
Views: 2,388
Posted By reema
Post Trinity-Duplicate removal

Dear All,

I am using trinity for transcriptomics assembly. I have few queries:-

1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files...
Forum: Bioinformatics 02-13-2014, 08:13 AM
Replies: 6
Views: 2,011
Posted By reema
Post Trinity-Duplicate removal

Dear All,

I am using trinity for transcriptomics assembly. I have few queries:-

1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files...
Forum: Bioinformatics 02-12-2014, 09:58 AM
Replies: 17
Views: 10,517
Posted By reema
Smile Trinity-duplicate removal

Dear All,

I am using trinity for transcriptomics assembly. I have few queries:-

1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files...
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