Forum: Bioinformatics
10-23-2015, 04:22 AM
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Replies: 4
Views: 1,945
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Forum: Bioinformatics
10-20-2015, 09:05 AM
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Replies: 4
Views: 1,945
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...
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Forum: Sample Prep / Library Generation
09-10-2015, 08:00 AM
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Replies: 2
Views: 1,471
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Forum: Sample Prep / Library Generation
09-09-2015, 07:42 AM
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Replies: 2
Views: 1,471
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Forum: Bioinformatics
06-30-2015, 08:09 AM
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Replies: 15
Views: 10,873
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...
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Forum: Bioinformatics
06-30-2015, 05:56 AM
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Replies: 15
Views: 10,873
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Forum: Bioinformatics
06-16-2015, 03:14 AM
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Replies: 1
Views: 1,383
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...
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Forum: Bioinformatics
03-24-2015, 03:42 AM
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Replies: 15
Views: 10,873
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...
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Forum: Bioinformatics
03-12-2015, 06:45 AM
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Replies: 15
Views: 10,873
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...
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Forum: Bioinformatics
02-25-2015, 03:23 AM
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Replies: 0
Views: 1,160
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Forum: Bioinformatics
12-15-2014, 12:45 AM
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Replies: 155
Views: 70,509
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...
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Forum: Bioinformatics
12-12-2014, 03:34 AM
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Replies: 155
Views: 70,509
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.
...
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Forum: Bioinformatics
11-27-2014, 05:55 AM
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Replies: 189
Views: 77,082
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...
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Forum: Bioinformatics
11-26-2014, 05:30 AM
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Replies: 189
Views: 77,082
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:
...
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Forum: Bioinformatics
10-15-2014, 05:40 AM
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Replies: 7
Views: 8,078
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Forum: Bioinformatics
10-14-2014, 07:03 AM
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Replies: 7
Views: 8,078
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...
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Forum: Bioinformatics
10-14-2014, 06:34 AM
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Replies: 7
Views: 8,078
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...
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Forum: Bioinformatics
08-07-2014, 08:56 AM
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Replies: 7
Views: 2,368
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...
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Forum: Bioinformatics
08-07-2014, 03:57 AM
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Replies: 7
Views: 2,368
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...
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Forum: Sample Prep / Library Generation
01-15-2014, 09:40 AM
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Replies: 0
Views: 1,312
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...
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