#HTseq

#RNASeq: what happens to multi-mapping reads? Whoah apparently #htseq and #featureCounts ignore them by default! #Salmon, #Sailfish and #Kallisto are the way, with the Expectation Maximization algorithm! @LabMutwil was right!!!

1/ Do you need reference sequence files from #Ensembl? All of the different files available can be confusing. Here’s a thread to help you decide which files you need…🧵 #genomics #bioinformatics #tweetorial #Ensembltraining🧬

14/ This file is best used for performing sequence similarity searches where patch and haplotype sequences would confuse analysis. If the primary assembly file is not present, that indicates that there are no haplotype/patch regions, and the 'toplevel' file is equivalent.

15/ If you are performing alignments using a program that requires a genome FASTA, such as #HTseq, TopHat or #HISAT then the best choice for most cases is the primary assembly.

HTSeq.Count (using #HTSeq 0.11.2 ) is now available on GenePattern Cloud ( #bioinformatics #RNASeq #quantitation

Analysing high-throughput sequencing data in Python with HTSeq 2.0. #HTseq #SequencingData #DataAnalysis #Python #Bioinformatics