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Results tagged with rna-seq
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user 926
Questions should include this tag if they pertain to issues related to bioinformatics analysis of RNA-seq data, e.g. normalization, differential expression analysis, sequencing and experimental design or transcriptome assembly...
3
votes
1
answer
850
views
ribo interval list for picard ensembl mm9 gtf
Could some one please help me with understanding how to generate the ribosomal interval list that is required to when using picard metrics this step
java -jar picard.jar CollectRnaSeqMetrics \
…
5
votes
0
answers
340
views
Annotating splice junctions from tophat/STAR output
Is there a way to annotate the splice junctions output from tophat/STAR output?
What I mean by annotate is can I know if it was involved in an alternative splicing event say skipped exon, MXE or ret …
16
votes
2
answers
25k
views
Difference between CPM and TPM and which one for downstream analysis?
What the difference between TPM and CPM when dealing with RNA seq data?
What metrics would you use if you have to perform some down stream analysis other than Differential expression for eg.
Cluste …
1
vote
1
answer
81
views
differential expression multiple studies
I was wondering if we can perform differential expression on samples from different library and read lengths.
What we intend to do is,
n = 6 tumors (recently sequenced using Hiseq 2500 read lengt …
2
votes
1
answer
7k
views
Error in checkFullRank(modelMatrix) deseq2
Trying to use deseq2 for differential expression analysis (rna-seq) between three groups and also account for batch effect as the control were sequenced at a different time point.
control: con
samp …
5
votes
1
answer
591
views
cell type specific genes - heatmap using rank based approach
I was wondering if some one can help me with pseudo r code for my approach here based on this paper to plot a heatmap
Figure 3
Figure description
The top 40 enriched genes percelltypeare shown in a h …
7
votes
2
answers
570
views
differential gene expression complex design no replicates
We have an experimental design as seen below
Where we administered drug at 0 min for each mouse genotype and took them down at given below intervals. wt and ko mouse models were administered only w …
7
votes
1
answer
716
views
insert size pre and post trimming
I have a problem here with my rna seq data:
Sequencing details:
rRNA was removed, followed by cDNA preparation and generation of stranded libraries using the TruSeq Stranded Total RNA Sample Prep Kit. …
4
votes
5
answers
4k
views
using python to write bioinformatics pipelines tutorial
I was wondering if there is a tutorial or a small code snippet to understand how to write bioinformatics pipeline using python, for example
use a aligner (say hisat)
get the output and process it u …