安裝中文字典英文字典辭典工具!
安裝中文字典英文字典辭典工具!
|
- HISAT2: RNA strandedness - Bioinformatics Stack Exchange
According to the help produced when I type hisat2 --help, the default strandedness when running HISAT2 is unstranded: --rna-strandness <string> specify strand-specific information (unstranded)
- rna seq - Classical alignment with HISAT2 - Bioinformatics Stack Exchange
samtools view -Sb hisat2 ${sample}_hisat2 sam | samtools sort > hisat2 $ {sample}_hisat2_sorted bam samtools index hisat2 ${sample}_hisat2_sorted bam rm hisat2 $ {sample}_hisat2 sam # Remove the sam files for storage purposes done # Quantifying Aligned reads using the Subread package's script 'featureCounts' for sample in $(cat sample_ids
- Hisat2 : which option should mention for strand specific library read . . .
I was trying hisat2 I get confused by the strand options The question has been already asked on github here but didn't get any satisfactory answer I'm surprise how much this strand information could be confusing in different tools Looking at the hisat2 manual I get confuse by the two different options:--rna-strandness
- HISAT2 - are all multi mapped reads reported by default?
HISAT2 searches for up to N distinct, primary alignments for each read, where N equals the integer specified with the -k parameter Primary alignments mean alignments whose alignment score is equal or higher than any other alignments It is possible that multiple distinct alignments have the same score
- hisat2 --rna-strandness option and downstream htseq-count analysis
I have a paired-end stranded sequencing library that was aligned to the genome using hisat2 without specifying the --rna-strandness (in other words, the default unstranded was the usage) Following this, the reads were assigned to genes using htseq-count and this time -s reverse was specified given the strand-specific sequencing assay type
- phylogenetics - TopHat2 versus HISAT2 inner workings - Bioinformatics . . .
To solve this issue, both TopHat2 and HISAT2 chop up the unmapped reads into around 25bp fragments Then: "TopHat2 tries to align many fragments from each read using all possible exons as the search space HISAT2 focuses on one fragment from each read, and once that fragment has been anchored it only searches locally "
- How can I bypass out of memory problem using a HISAT2 for human . . .
Stack Exchange Network Stack Exchange network consists of 183 Q A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers
- python - A . gtf file for HG38 for HISAT2 indexing - Bioinformatics . . .
Stack Exchange Network Stack Exchange network consists of 183 Q A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers
|
|
|