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Forum: Bioinformatics 04-03-2018, 06:09 AM
Replies: 0
Views: 425
Posted By Slacanch
developmental trajectories with Wanderlust

Hey all,
I am looking for an implementation of "wanderlust" an algorithm produced by Dana Pe'er's lab to find developmental trajectories in single cell RNA seq. Unfortunately, all pages linked to...
Forum: Bioinformatics 05-08-2017, 12:27 AM
Replies: 0
Views: 1,724
Posted By Slacanch
Hisat2 reporting of uniquely mapped reads

Recently i've been optimising Hisat2 to work with the latest version of the human genome. According to its manual, Hisat2 reports the number of valid alignments within the tag NH:i:N, where N is the...
Forum: RNA Sequencing 09-08-2015, 04:42 AM
Replies: 1
Views: 3,081
Posted By Slacanch
Mean-variance relationship in RNA-seq

hey all,
i am plagued by a problem regarding the mean-variance relationship in RNAseq experiments, hopefully you can help me with this.

according to most analysis tools i've used, rna-seq data...
Forum: Bioinformatics 01-20-2015, 08:20 AM
Replies: 2
Views: 1,213
Posted By Slacanch
well i don't really care about the sequence, it's...

well i don't really care about the sequence, it's for profile comparison.
as long as the positions are right, i'm ok with it.

maybe i shouldn't have called it pileup, but coverage. just a measure...
Forum: Bioinformatics 01-20-2015, 07:39 AM
Replies: 2
Views: 1,213
Posted By Slacanch
generating pileup of paired end fragments

Dear all,
i'm working with paired end rnaseq data. i wanted to generate a pileup with samtools mpileup but noticed that only the mapping reads get counted, and not the unmapped part between two...
Forum: Bioinformatics 01-19-2015, 04:30 AM
Replies: 5
Views: 2,286
Posted By Slacanch
ooooh, so the value would be 1 everywhere but...

ooooh, so the value would be 1 everywhere but because of floating point approximation shenanigans it turns out to be 0.99 bla bla.

it makes sense, i tried other correction methods and they all...
Forum: Bioinformatics 01-19-2015, 04:20 AM
Replies: 5
Views: 2,286
Posted By Slacanch
I am well aware of the consequences of having no...

I am well aware of the consequences of having no replicates, as it has rightly been stated in multiple threads already :)

i just find it odd that every single adjusted p-value has the same exact...
Forum: Bioinformatics 01-18-2015, 11:45 PM
Replies: 5
Views: 2,286
Posted By Slacanch
DEseq2 gives constant adjusted p-values

I am doing some exploratory analyses on two datasets without replicates. i found it strange that irrespective of the calculated p-value, the adjusted p-value has constant value across all features....
Forum: General 10-16-2014, 05:59 AM
Replies: 0
Views: 948
Posted By Slacanch
Angry PAR-clip T to C mutations become T to G in the minus strand in IGV?

I am looking at some PAR-clip data. trimming and mapping went perfectly, however, when i look at the data on IGV, in the plus strand i have a vast majority of T to C mutations (as expected), but in...
Forum: Bioinformatics 11-06-2013, 12:57 AM
Replies: 2
Views: 1,469
Posted By Slacanch
Question SGD liftOver chain files issue

SGD (Saccharomyces Genome Database), contains a repository of liftOver chain files that allow to convert form any version of the reference genome to the last one.

after trying, and failing...
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