SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 107
Search took 0.01 seconds.
Search: Posts Made By: jmwhitha
Forum: Bioinformatics 08-13-2020, 03:04 AM
Replies: 334
Views: 147,083
Posted By jmwhitha
Good morning, It seems that the aqhist for...

Good morning,

It seems that the aqhist for my raw fastq file has the same dip at Q35. So, please disregard the previous questions. If you could tell me if peaks and dips are common or not...
Forum: Bioinformatics 08-12-2020, 08:09 AM
Replies: 334
Views: 147,083
Posted By jmwhitha
Good afternoon Brian and GenoMax, Hope you...

Good afternoon Brian and GenoMax,

Hope you two are doing well all things considered :)

I have many metagenomes to assemble these days and am trying to make fewer and longer scaffolds and reduce...
Forum: Metagenomics 11-09-2016, 03:34 AM
Replies: 0
Views: 1,994
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: 1,573
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: 1,573
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: 1,573
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: 24,453
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: 24,453
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: 24,453
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: 24,453
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: 2,260
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: 2,260
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: 2,260
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: 8,396
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: 8,396
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: 8,396
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: 4,691
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: 6,643
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: 4,691
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: 4,691
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: 4,691
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: 4,691
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: 8,597
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: 4,065
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: 4,065
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.
Showing results 1 to 25 of 107

 


All times are GMT -8. The time now is 04:08 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO