Dear all ,
I tried to use eXpress to count the mapping results obtained with Bowtie2.
The command used is
express -m 450...
12 results in 0.0070 seconds.
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Bug with eXpress: Unable to open input SAM file
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how can I get abundance from both Iso-seq output and illumina data?
Hi,
We've got the done the RNA-seq of a species (genome is about 3GB), but NO reference genome is available, using pacbio and Illumina. After the... -
Memory requirments for eXpress
Does someone know how much memory eXpress usually consumes? (https://github.com/adarob/eXpress)
I am using eXpress together with kma (... -
RNA seq analysis - small number of genes
Hi all,
I am new to RNA seq analysis and want to look at the expression of a small number of genes (8) in some publicly available RNA seq... -
gene FPKM from eXpress
Hello,
I want to calculate gene-level FPKM values from eXpress data. From eXpress output, I have FPKM values for each isoform of a gene.... -
relative isoform abundance in eXpress
Hello,
I don't know how to calculate "relative" isoform abundance (proportions) for each gene from the eXpress output. One (naive)... -
DESeq2 for isoform level
Hello,
(1) I was wondering whether DESeq2 is appropriate to test for differentially expressed isoforms? If we have raw counts (on isoform... -
Bowtie2 / eXpress
Hi,
I was planning to use Bowtie2 to align RNAseq reads to a list of transposable elements and I wondered which could be the best option... -
Which tool should I use to summarize counts from BWA-mem?
From what I read, BWA-mem is one of the best alignment tools (at least for de novo transcriptomes).
However, it seems that summarization... -
Error with RSEM/eXpress/cufflinks
Hi All! Hopefully someone can help me here, I'm trying to quantify expression from bowtie2 output.
When I try to used RSEM/eXpress, it fails because...Last edited by bob-loblaw; 05-31-2013, 07:16 AM. -
RNA-seq and sense/antisense expression differences
Hello all,
Wondering if anyone out there could de-mystify the inner working of eXpress and edgeR for me or give me a better suggestion... -
Any experience with eXpress?
Hello.
We are doing some environmental RNA sequencing from an Antarctic time series. I have some prelim data from a HI Seq run, full multiplexed...
