seqcluster
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lpantano
small RNA analysis from NGS data
Hello, I am wondering about the following call to seqcluster that I found in a pipeline: ` seqcluster collapse -f reads -m 1 --min_size 15 -o some_folder` What do the...
https://github.com/lpantano/seqcluster/blob/38297c9b158a260da4fef561fefe831892e2544d/seqcluster/make_clusters.py#L50
Hi, Just a heads up :) link to seqcluster's github is misspelled. https://github.com/lpantano/seqclsuter Thought, you might want to change that ;)
Hi there! I am currently using seqcluster to do some pipeline analysis on small RNAs, which requires me to extract some information that is embedded in the json output for...
Hello, This file is apparently auto-created during tests and does not go away when cleaning the source tree. Cheers, Steffen
Hi, I like the report about mirQC you have shown in here: https://github.com/lpantano/mypubs/blob/master/srnaseq/mirqc/ready_report.md Mostly, I wanted to create a barplot which has contribution of each type of RNA. As suggested...
I was running a smallRNA analysis on bcbio, and was expecting the output to be like previous analyses I have carried out, where each isomir is specified according to your...
#####command：bin/conda install seqcluster bcbio-nextgen -c bioconda Fetching package metadata: ...... Solving package specifications: . Error: Dependencies missing in current linux-64 channels: - bcbio-nextgen -> ipdb - bcbio-nextgen -> arrow Did...
think about it: https://www.ncbi.nlm.nih.gov/pubmed/27307639
Hi Lorena ! I found a new issue with seqcluster using the following command line : /usr/local/bin/seqcluster collapse -f file.fastq -o out_collapse Here the error message : Traceback (most recent...
