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Forum: Bioinformatics 12-06-2017, 07:16 PM
Replies: 3
Views: 1,449
Posted By analog900
Thanks! This might just work. I'll look into it....

Thanks! This might just work. I'll look into it. Thanks again! Appreciate it!
Forum: Bioinformatics 11-29-2017, 10:05 AM
Replies: 3
Views: 1,449
Posted By analog900
Decoding DNA barcodes within PCR amplicons

Hi all,

Has anybody experience with decoding barcoded DNA sequences? We're sequencing PCR amplicons, all identical except for a (custom) 10nt barcode, flanked by transgenic cassettes.

Like...
Forum: Bioinformatics 08-23-2017, 03:38 PM
Replies: 0
Views: 957
Posted By analog900
Genome-guided transcriptome assembly on single cell RNA-seq

Hi all,

I'm doing single cell RNA-seq and I'm interested in running genome-based transcriptome assembly (or de novo if necessary). The idea is that we would supplement existing GTFs in case there...
Forum: Bioinformatics 01-03-2016, 01:29 PM
Replies: 8
Views: 4,676
Posted By analog900
Hi Alex, Thanks so very much for your help. I'm...

Hi Alex,
Thanks so very much for your help. I'm still running a few more runs, but it does indeed help. In my own samples the decrease in percentage (no-feature) is not quite as dramatic as in the...
Forum: Bioinformatics 12-23-2015, 04:25 PM
Replies: 8
Views: 4,676
Posted By analog900
Hi Alex, I downloaded UCSC mm10 from here: ...

Hi Alex,

I downloaded UCSC mm10 from here:

http://cole-trapnell-lab.github.io/cufflinks/igenome_table/index.html

and downloaded "control data" from here:...
Forum: Bioinformatics 12-23-2015, 01:16 PM
Replies: 8
Views: 4,676
Posted By analog900
Hi Alex, Thanks for replying! See below...

Hi Alex,
Thanks for replying!

See below the first few lines from ReadsPerGene and afterwards the Log.final.out

ReadsPerGene:
N_unmapped 55905 55905 55905
N_multimapping 48816 48816 48816...
Forum: Bioinformatics 12-23-2015, 12:52 AM
Replies: 8
Views: 4,676
Posted By analog900
Getting very low numbers of annotated reads from STAR/mm10

Hi all,
I'm trying to analyze RNA-seq data (mouse, multiplexed Nextera XT libraries) using STAR and I'm having the problem that I'm getting mostly "no feature" and hardly any annotated reads...
Forum: RNA Sequencing 01-20-2015, 09:56 AM
Replies: 12
Views: 3,239
Posted By analog900
Thanks so much guys! Working through the...

Thanks so much guys!
Working through the DESeq2 vignette now and learning new stuff... really excited!
Thanks again!
Forum: RNA Sequencing 01-16-2015, 01:12 PM
Replies: 12
Views: 3,239
Posted By analog900
Thank you. Really appreciate it! Can you...

Thank you. Really appreciate it! Can you recommend any other standard/accepted pipelines downstream of featureCounts?
Forum: RNA Sequencing 01-16-2015, 10:51 AM
Replies: 12
Views: 3,239
Posted By analog900
I've been loosely following the "simple fool's...

I've been loosely following the "simple fool's guide for rna seq" by the group of Stephen Palumbi (http://sfg.stanford.edu/guide.html). They parse their SAM output files with a series of python...
Forum: RNA Sequencing 01-16-2015, 09:47 AM
Replies: 12
Views: 3,239
Posted By analog900
Using featureCounts gives me nice summary and...

Using featureCounts gives me nice summary and counts text files. However, my SAM and BAM files still contain the original, genomic, annotations (obviously). Ideally, I would like to convert the...
Forum: RNA Sequencing 01-15-2015, 03:28 PM
Replies: 12
Views: 3,239
Posted By analog900
Thanks guys!! Appreciate it! I'll give it a try. ...

Thanks guys!! Appreciate it! I'll give it a try.
Thanks again!
Forum: RNA Sequencing 01-15-2015, 03:03 PM
Replies: 12
Views: 3,239
Posted By analog900
Newbie question regarding mapping of RNA-seq data

Hi all,
I'm stuck with a total newbie problem here. I'm analyzing RNA-seq data from mouse, I mapped the (paired-end) sequences using TopHat against mm9 (using bowtie1) but when I look at the SAM...
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