bioinformatics-workbook

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Ephantus-Wambui

molecules

I would like to add here a part about using Edirect to retrieve data =from NCBI repositories, scripts will be provided to query nuccore, assembly, gene.. databases.

SolayMane

fastq-dump parallel error in tutorial

1

Thanks for this great resource. `fastqc-dump` is fairly poorly documented so this workbook was a great starting point for me. I think there is a small error on: https://bioinformaticsworkbook.org/dataAcquisition/fileTransfer/sra.html#gsc.tab=0 `parallel...

Koen-vdl

Removed backslash before pipe symbol because, unlike on Github, on the web page it actually shows up as \| instead of just |

molecules

Changed --format to -format (yes, single dash). Used "tail -n +2" to skip the first line which would otherwise contain the word "Run". Changed three colons to four so that...

molecules

Update UnixCheatSheet.md

1

Removed extraneous words "found at found here" -> "found here"

molecules

Hi Jennifer, Thanks for writing the awesome tutorial! I found you wrote "Optionally you could subset to only genes that are differentially expressed between groups." in this WGCNA tutorial. However,...

JasonTan-code

Confirm that use of BLAST's `-max_target_seqs` is intentional

1

Hi there, This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's `-max_target_seqs` parameter: - [dataAnalysis/RNA-Seq/annotating-transcripts.md](https://github.com/ISUgenomics/bioinformatics-workbook/blob/2210a7ebab4eb15d2ba40d24d3ed326a4d187f78/dataAnalysis/RNA-Seq/annotating-transcripts.md)...

armish

Just a minor update as title.

hsiaoyi0504