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Dear bcbio community,
In 2011, the Harvard Chan Bioinformatics Core began developing bcbio as an open-source framework to tackle challenges in reproducibility and scalability in the field of next-g…
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Per [@jashapiro's comment](https://github.com/AlexsLemonade/refinebio-examples/pull/267#pullrequestreview-509594046) on PR #267 handling the addition of the RNA-seq ortholog mapping analysis to the re…
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For GTEx V7 data we've done imputation and rna-seq normalization, and we have PCA analysis results from Broad. PEER analysis is still running. Once we have the result we should have the material to do…
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_From https://github.com/AlexsLemonade/training-modules/issues/515#issuecomment-1058472857_
The following cheatsheets still need updates to match the changes in #521.
- [ ] [RNA-seq-cheatsheet…
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Hello members,
I am currently working with TPM expression data obtained from RNA-seq analysis, and my dataset includes a diverse range of biotypes such as miRNA, lncRNA, pseudogenes, etc., resultin…
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- [ ] check the runinfo to make sure the sample can be combined (i.e. same pairedness, insert size, read length)
- [ ] make sure we don't process the same file twice
- [ ] concatenate output file…
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In the Signac vignette "Analyzing PBMC scATAC-seq", there is a step in which we filter out those features falling in chromosome scaffolds or other sequences instead of the standard chromosomes:
``…
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```bash
#!/bin/bash
script=/mnt/users/fabig/cluster_pipelines/RNAseq-analysis/RNA_map.sh
fdir=/mnt/SeqData1/bovine/ullevaal_cow_rna_nov_2016/sample_pool
genome=/mnt/users/tikn/seqdata1/bovine/…
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**DO NOT INCLUDE REQUESTS IN THE FIRST COMMENT.**
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# General Notes
This repository serves as a mostly automated p…
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### Description of feature
Hi, I couldn't run the pipeline on some smart-seq datasets which contains only single-end fastq files. I tried with two different samplesheets and get an error that fastq_2…