salmon

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Would alevin work with QIAseq UPX 3' protocol?

1

knokknok

Trying to make an index but twopaco_tmp doesn't change or grow, seems stuck in Round0, Salmon doesn't use swap

2

Hello, I'm trying to create an index file with salmon (version 1.4.0) according to this tutorial here: https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/ (because I would like to find isoforms using isoformSwitchAnalyseR and the salmon...

DobbyLikesPenguins

libboost shared library error

9

I installed salmon from conda environment using python3 and got the below error: ``` $ salmon salmon: error while loading shared libraries: libboost_thread.so.1.60.0: cannot open shared object file: No such...

bounlu

salmon: symbol lookup error: salmon: undefined symbol: _ZN5boost15program_options3argE

1

I am using Ubuntu on my laptop. I installed salmon by the command:- conda install --channel bioconda salmon I downloaded the SalmonTools scripts from git clone https://github.com/COMBINE-lab/SalmonTools.git But I am...

shrisauhard

Salmon after STAR alignment

1

Hi, this problem was considered in issue 104 and I have been following the instructions given there. I am running Salmon in alignment mode on bam files generated by STAR...

JennyFrodoBrynnNick

Conda dependency conflict with ICU between Salmon 1.3.0 and R 4.0.3

1

This isn't strictly speaking a bug with salmon per-se, but when installing salmon from conda, its impossible to have both R 4.0.3 and Salmon 1.3.0 installed in the same environment...

ACastanza

Using salmon quantification with DeSeq2

17

Hi, I run salmon then used quantmerge to combine the results as `salmon quantmerge --quants `cat list_of_quant_folders` --column numreads -o Merged_quants.txt ` Can I use this as input for the...

thkitapci

Hi, The data I currently have is quantified by salmon. But it was organized into a text file (row name is the ID of the gene, and the column name...

authentic-zz

Hi @rob-p and all, Thank you for the wonderful tool. I've been using Salmon for some time now, and have encountered a question. How is Salmon affected by different read...

roni-fultheim

Hi Rob, Thanks for developing such a good tool for the community. I really like it! Recently, I found that Salmon gave higher mapping rate than Hisat2 when I didn't...

yichangyu