I run this command:
hisat2 -p 40 -q -x Ene_index --sra-acc SRR13696274 --al alignedRNA_1 -S alignment1
and the output says:...
41 results in 0.0024 seconds.
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Hisat2 output is empty
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Parallelising Hisat2
I need to run Hisat2 on 36 paired-end files. The files are labelled like:
file1_1.fq
file1_2.fq
file2_1.fq
file2_2.fq
... -
Refernece Genome for Wheat (Rna-seq) with Hisat2
How can i Download Reference genome of Wheat (triticum aestivum) as index for mapping (with RNA-seq) by HISAT2.
The file i accessed from NCBI... -
Transcriptome construction
Hello all
I wanted to ask that whether i can use both genome and transcriptome (generated using PacBio) as reference together and align... -
Htseq_processing double number of aligned reads
Hi All,
I am trying to generate count data from the bam files using Htseq. Our data was produced using Illumina stranded library and sequenced... -
HISAT2: a surprising read shows up in alignment results
I was spot-checking the output of alignment results from HISAT2 and noticed one read (CATCTTGTTTCACACTAGTCACATTCTTGTTTTAAGTGCCTTTAGTTTTAACAGTTCACTTTTTACAGTACTATTT... -
Running STAR on Windows WSL
WSL can be a great option for those that need to have a Windows OS and cannot access a Linux server.
I have tried to run STAR from Windows WSL... -
Hisat2 index with splice sites
Hello,
I would like to detect lncRNAs from RNA-seq data. Initially, I'm using Hisat2 for aligning the samples. For this I downloaded the... -
Hisat2: no command found in bash
Hi all,
I'm a complete novice at RNAseq mapping and I am trying to follow this protocol using their data: https://www.nature.com/nprot/journal... -
hisat2 multi-threading problem.
As best I can see, this should be working. I've got 16 cores:
...Code:$ grep -c ^processor /proc/cpuinfo 16
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Hisat2 multithreading not working.
As best I can see, this should be working. I've got 16 cores:
...Code:$ grep -c ^processor /proc/cpuinfo 16
-
Hisat2 multithreading not working.
As best I can see, this should be working. I've got 16 cores:
...Code:$ grep -c ^processor /proc/cpuinfo 16
-
HISAT2: advantages of build index using annotated transcripts
Hello,
after reading the paper, I am still not sure about what is the advantage of building an index for HISAT2 by calling hisat2-build with...Last edited by dekontrol; 06-22-2017, 10:46 PM. -
Align full length contigs instead of reads
Hello,
Splice aligners like HiSAT2 and STAR are optimised to map short reads (~100bp) to large genomes. I have assembled contigs available.... -
Hisat2 reporting of uniquely mapped reads
Recently i've been optimising Hisat2 to work with the latest version of the human genome. According to its manual, Hisat2 reports the number of valid...
