SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 20 of 20
Search took 0.00 seconds.
Search: Posts Made By: travelk
Forum: Bioinformatics 10-23-2015, 04:22 AM
Replies: 4
Views: 1,945
Posted By travelk
Ok, I've tested it, and RSeQC is exactly the type...

Ok, I've tested it, and RSeQC is exactly the type of thing I was looking for. I need to modify it slightly to suit my purposes but it lets me automate the verification of my genes of interest.
...
Forum: Bioinformatics 10-20-2015, 09:05 AM
Replies: 4
Views: 1,945
Posted By travelk
Test for read coverage uniformity of genes?

Does anyone know of a program/package/method to test coverage uniformity of reads over individual genes?

My differential expression analysis shows 1500 genes... but when I look closer at IGV, I...
Forum: Sample Prep / Library Generation 09-10-2015, 08:00 AM
Replies: 2
Views: 1,471
Posted By travelk
Thanks for the response! I don't do a DNase...

Thanks for the response!

I don't do a DNase step because I use the Fluidigm C1 system and it's done within the chip in the machine. The tech sheet specifically states:...
Forum: Sample Prep / Library Generation 09-09-2015, 07:42 AM
Replies: 2
Views: 1,471
Posted By travelk
Genomic Contamination with Clontech PolyA selection?

Hi Everyone,

I am working with single cell RNA-Seq and am currently analyzing my data. I've noticed that I often get a lot of reads aligning to the UTR but not at all to the exons. When I look...
Forum: Bioinformatics 06-30-2015, 08:09 AM
Replies: 15
Views: 10,873
Posted By travelk
I think the original purpose of the Ambion...

I think the original purpose of the Ambion spike-ins was purely as a control to ensure that the lysis buffer was getting to all the wells in the C1 chip and that the RT was working efficiently for...
Forum: Bioinformatics 06-30-2015, 05:56 AM
Replies: 15
Views: 10,873
Posted By travelk
The issue of normalization in single cell RNA-seq...

The issue of normalization in single cell RNA-seq seems to still be a topic up for debate. The 92 ERCC spike-ins seem to be the gold standard for now and a lot of the big groups who are advancing the...
Forum: Bioinformatics 06-16-2015, 03:14 AM
Replies: 1
Views: 1,383
Posted By travelk
Spearman correlation test: FPKM or counts?

I'm not sure if this is very obvious but I'm not a statistician so I thought I would confirm with the more knowledgeable people on this site.


I would like to do a Spearman correlation between...
Forum: Bioinformatics 03-24-2015, 03:42 AM
Replies: 15
Views: 10,873
Posted By travelk
Thank you for your input! Sometimes it's...

Thank you for your input!

Sometimes it's just reassuring to have someone else confirm that what you are doing isn't completely off base. I've checked out the scde package like you suggested and...
Forum: Bioinformatics 03-12-2015, 06:45 AM
Replies: 15
Views: 10,873
Posted By travelk
Normalization in single cell RNA-seq data

Hi All,

I've been testing various differential expression analyses on my single-cell RNA-Seq data either using FPKM (generated by Cufflinks, used with Fluidigm Singular Analysis Toolset or...
Forum: Bioinformatics 02-25-2015, 03:23 AM
Replies: 0
Views: 1,160
Posted By travelk
Best way to build a modified transcriptome gtf model?

Hi Everyone,

When I align my reads with tophat against the GRCm38.fa and then use various programs (including Cufflinks) to match them to known features using the Ensembl gtf file, many of my...
Forum: Bioinformatics 12-15-2014, 12:45 AM
Replies: 155
Views: 70,509
Posted By travelk
Sorry, I worded it poorly. Indeed, I provided...

Sorry, I worded it poorly. Indeed, I provided STAR with a fasta file to generate the genome files it aligns my reads to which would suggest it is genome based. To clarify, I provide the exact same...
Forum: Bioinformatics 12-12-2014, 03:34 AM
Replies: 155
Views: 70,509
Posted By travelk
Hi Everyone, I have a quick fundamental...

Hi Everyone,

I have a quick fundamental question about featureCounts.

I ran my reads through STAR and used featureCounts to get the counts of reads to that were successfully aligned.
...
Forum: Bioinformatics 11-27-2014, 05:55 AM
Replies: 189
Views: 77,082
Posted By travelk
Ok, I re-ran the files using the exact same...

Ok, I re-ran the files using the exact same script on the exact same files as suggested to check if it happened consistently on the same line... but now there is no problem with the new output files...
Forum: Bioinformatics 11-26-2014, 05:30 AM
Replies: 189
Views: 77,082
Posted By travelk
Hey everyone, I've used trimmomatic to clean...

Hey everyone,

I've used trimmomatic to clean up my reads but when I use the cleaned files in tophat, I get an error. When I examined a bit closer I discovered that trimmomatic converted this:
...
Forum: Bioinformatics 10-15-2014, 05:40 AM
Replies: 7
Views: 8,078
Posted By travelk
Ok, I checked with cutadapt and indeed, I hadn't...

Ok, I checked with cutadapt and indeed, I hadn't trimmed them properly for paired data. I reran the STAR alignment and it worked. Thank you all for taking the time to help me.

As a note, I...
Forum: Bioinformatics 10-14-2014, 07:03 AM
Replies: 7
Views: 8,078
Posted By travelk
I trimmed two adapters based on the...

I trimmed two adapters based on the overrepresented sequences found by FastQC: the Nextera barcodes and a primer used during the cDNA synthesis.

cutadapt -q 10 -a...
Forum: Bioinformatics 10-14-2014, 06:34 AM
Replies: 7
Views: 8,078
Posted By travelk
STAR with trimmed reads

Hi Everyone,

I am doing a comparison of tophat2 vs STAR alignment of my RNA-seq data, and trimmed vs untrimmed data. (I was getting different results using tophat2 than the bioinformaticians were...
Forum: Bioinformatics 08-07-2014, 08:56 AM
Replies: 7
Views: 2,368
Posted By travelk
Thank you! This totally did the trick. I...

Thank you! This totally did the trick. I processed the files and then reran them through fastq_screen and all the E.coli reads were gone.

And thank you a.kmg and GenoMax for your clear step by...
Forum: Bioinformatics 08-07-2014, 03:57 AM
Replies: 7
Views: 2,368
Posted By travelk
Removing contaminating reads

Hey all,

I have a very basic question that I just cannot seem to find a straight answer to despite scouring Google and SEQanswers.

When I ran my dataset through Fastq_screen I discovered I have...
Forum: Sample Prep / Library Generation 01-15-2014, 09:40 AM
Replies: 0
Views: 1,312
Posted By travelk
Miltenyi Microbeads + Nextera DNA Sample Prep

Hi All,

I've been having some trouble purifying my cells by FACS and have been considering moving to the Miltenyi microbead sorting system. I'm trying to figure out whether the magnetic beads...
Showing results 1 to 20 of 20

 


All times are GMT -8. The time now is 02:48 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO