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Forum: Metagenomics 11-09-2016, 03:34 AM
Replies: 0
Views: 1,062
Posted By jmwhitha
Multithread MyCC

Dear SeqAnswers community,

Can someone please tell me how to multithread MyCC? I don't see any options in the documentation. Not sure if this has to do with it coming in a virtualbox.

Thank you...
Forum: RNA Sequencing 09-14-2016, 02:36 PM
Replies: 2
Views: 924
Posted By jmwhitha
Found the following messages at...

Found the following messages at https://groups.google.com/forum/#!topic/rsem-users/GoWPrFzMHMI, which brought up a new question- Multiple genes reside on one transcript. Is designating...
Forum: RNA Sequencing 09-14-2016, 01:49 PM
Replies: 2
Views: 924
Posted By jmwhitha
So, I just removed everything but "CDS" and...

So, I just removed everything but "CDS" and "gene" lines in my GFF3 file. rsem-prepare-reference gave a no attribute error. Then, I removed "gene" too and I got the error "reference contains no...
Forum: RNA Sequencing 09-14-2016, 01:02 PM
Replies: 2
Views: 924
Posted By jmwhitha
GFF3 formatting wrong for RSEM?

Hello SEQanswers community,

When I run rsem-prepare-reference with refseq it only captures "tRNA" in my gff3 file. I only realized this issue because the output from rsem-calculate-expression was...
Forum: RNA Sequencing 08-20-2016, 09:21 AM
Replies: 45
Views: 20,827
Posted By jmwhitha
Simon, Thanks again for your quick replies....

Simon,

Thanks again for your quick replies. I just wanted to mention that I really appreciate your last response. While you may not be interested, I wanted to describe for others at least how I...
Forum: RNA Sequencing 07-21-2016, 06:12 AM
Replies: 45
Views: 20,827
Posted By jmwhitha
Multi-fasta

Thank you very much for your fast reply! Yes, each contig/chromosome (aka @SQ) is actually a gene. The format of the multi-fasta file I used for my bowtie2 alignment is below. It's not a...
Forum: RNA Sequencing 07-20-2016, 06:12 PM
Replies: 45
Views: 20,827
Posted By jmwhitha
Does it have to do with my S?...

Does it have to do with my S? http://www-huber.embl.de/users/anders/HTSeq/doc/count.html says that "__no_feature: reads (or read pairs) which could not be assigned to any feature (set S as described...
Forum: RNA Sequencing 07-20-2016, 06:03 PM
Replies: 45
Views: 20,827
Posted By jmwhitha
Most of my reads are going to no_feature

Good evening SEQanswers community,

I am having issues with counting my reads using HTseq. I found this thread, but I was not able to use the same modifications to help my situation. First I sorted...
Forum: Bioinformatics 04-01-2016, 04:58 PM
Replies: 3
Views: 1,318
Posted By jmwhitha
Excuse me. I meant to say in step 3 3. For...

Excuse me. I meant to say in step 3
3. For cells which contain values less than 50, put 50. It's similar to something done by Chhabra et al. 2006 (doi:10.1128/JB.188.5.18171828.2006).
Forum: Bioinformatics 04-01-2016, 02:29 PM
Replies: 3
Views: 1,318
Posted By jmwhitha
Hey SequencingJelly, Thanks for your reply....

Hey SequencingJelly,

Thanks for your reply. I was actually just about to implement the pipeline I arrived at today. Perhaps you can comment on it.

My planned steps are:
1. For each array, find...
Forum: Bioinformatics 01-24-2016, 02:17 PM
Replies: 3
Views: 1,318
Posted By jmwhitha
RMA Nimblegen Data

Hello SeqAnswers community,

I'm rather new to analyzing microarray data, so please forgive my ignorance. I have a couple of questions.

Can I RMA normalize the probe data in my excel worksheet...
Forum: Bioinformatics 12-15-2015, 07:06 PM
Replies: 5
Views: 1,165
Posted By jmwhitha
Thanks GenoMax! I'm actually not there anymore....

Thanks GenoMax! I'm actually not there anymore. I'm at ORNL now.
Forum: Bioinformatics 12-15-2015, 10:35 AM
Replies: 5
Views: 1,165
Posted By jmwhitha
Hello my friend! It's been a while :) ...

Hello my friend!

It's been a while :)

Sorry, I put "decent" because I don't actually know the sum he's received and my boss is out of country currently and will be difficult to reach until...
Forum: Bioinformatics 12-15-2015, 09:17 AM
Replies: 5
Views: 1,165
Posted By jmwhitha
Computer Shopping List

Hello SEQanswers community,

I am putting together a list of specs to purchase a new computer for my lab for doing everything from transcriptomics to de novo assembly to proteomics to metagenomics....
Forum: Bioinformatics 10-15-2014, 04:16 AM
Replies: 7
Views: 3,252
Posted By jmwhitha
I would still like to know how, but I ended up...

I would still like to know how, but I ended up using Tablet to confirm the mutations that were found when I did genome sequencing.

God bless,
Jason
Forum: Bioinformatics 09-26-2014, 08:50 AM
Replies: 10
Views: 5,793
Posted By jmwhitha
Hello Santi, I found a variety of issues...

Hello Santi,

I found a variety of issues with this pipeline so I went with DEGseq. Besides not having as many issues, the processing time was much faster. So, actually I'd recommend you try DEGseq...
Forum: Bioinformatics 05-12-2014, 11:47 AM
Replies: 7
Views: 3,252
Posted By jmwhitha
I also just saw that the reference in tview stops...

I also just saw that the reference in tview stops at around 1350 bases. What does that mean?
Forum: Bioinformatics 05-12-2014, 11:14 AM
Replies: 7
Views: 3,252
Posted By jmwhitha
Thank you for the suggestions swbarnes2. I agree...

Thank you for the suggestions swbarnes2. I agree that the N's make it seem like there is something wrong with the reference. My reference has a single header line and each subsequent line has 70...
Forum: Bioinformatics 05-08-2014, 08:25 AM
Replies: 7
Views: 3,252
Posted By jmwhitha
Thanks for your quick response Richard! I was...

Thanks for your quick response Richard! I was already home when I saw it though. Here's what I could get.

##"samtool flagstat" ##
samtool flagstat file.bam

11959974 + 0 in total (QC-passed...
Forum: Bioinformatics 05-07-2014, 01:18 PM
Replies: 7
Views: 3,252
Posted By jmwhitha
Calling SNPs from RNAseq bam files

Hello SeqAnswers community,

I am trying to use Samtools to call SNPs from my RNAseq data. I already have bam files, so I tried to use the following commands.

#Method 1 -
samtools sort...
Forum: Bioinformatics 12-05-2013, 05:50 AM
Replies: 8
Views: 7,348
Posted By jmwhitha
Hello Adam, I actually ended up using a...

Hello Adam,

I actually ended up using a simpler pipeline. I found too many mysteries with TopHat-Cufflinks...Cummerbund, the kind that you need faith for. Though I have faith in my Savior, to me,...
Forum: Bioinformatics 09-12-2013, 10:11 AM
Replies: 18
Views: 3,300
Posted By jmwhitha
Hello all, Despite two emails, I have not...

Hello all,

Despite two emails, I have not received any answers. I will look around for some knowledgeable computer scientists to give me a hand.

Thanks again and God bless,
Jason
Forum: Bioinformatics 08-30-2013, 03:21 PM
Replies: 18
Views: 3,300
Posted By jmwhitha
Thanks for the suggestion. I just sent them an...

Thanks for the suggestion. I just sent them an email. I'll let everybody know what comes of it.
Forum: Bioinformatics 08-30-2013, 07:34 AM
Replies: 0
Views: 1,017
Posted By jmwhitha
BAMBI inference of transcription factor binding sites

Good morning SeqAnswers Community,

I am trying to find binding site motifs for a transcriptional regulator. I have used MEME, and that gives me some potentials, but I wanted to try other software...
Forum: Bioinformatics 08-30-2013, 07:06 AM
Replies: 18
Views: 3,300
Posted By jmwhitha
Please help.

Please help.
Showing results 1 to 25 of 105

 


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