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Can HISAT2 be invoked in bash shell, and can it be fed variables or names with wildcards as inputs?
hisat2 shell batch jobs wild cards bash written 1 day ago by RNAseqer • 0 • updated 1 day ago by RamRS ♦ 20k
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Selecting methods for performing pairwise RNAseq analysis without replicates
tissues deseq2 deseq rna-seq hisat2 written 6 days ago by bioinforesearchquestions • 200 • updated 6 days ago by i.sudbery ♦ 3.8k
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Hisat2 -Can it align paired readfiles, and unpaired read files leftover from trimming/QC simultaneously?
alignment paired end rna-seq hisat2 written 13 days ago by RNAseqer • 0 • updated 13 days ago by h.mon ♦ 23k
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Reference sequence for indica Rice Paired End reads assembly using HISAT2
rice assembly referance indica hisat2 written 17 days ago by sharadlko1 • 0
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Hisat2 after the use of trimmomatic software: (ERR): hisat2-align exited with value 134
trimmomatic new tuxedo protocol rna-seq hisat2 written 22 days ago by swarajgaikwad15 • 0 • updated 22 days ago by ATpoint ♦ 13k
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132
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1
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Strange output of samtools flag stat?
mouse samtools rna-seq hisat2 written 26 days ago by heking • 0 • updated 26 days ago by Istvan Albert ♦♦ 79k
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2
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185
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Stringtie elimination of important transcripts
assembly stringtie alignment rna-seq hisat2 written 4 weeks ago by ra2967 • 10
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How to map RNA-seq with hisat2, stringtie, an assembly fasta, a gtf file, and a transcript fasta?
stringtie hisat2 mapping transcriptome written 5 weeks ago by O.rka • 70 • updated 5 weeks ago by swbarnes2 ♦ 4.8k
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6 follow
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RNA-Seq Differential Expression Bash Scripting Error
pipeline samtools bash scripting rna-seq hisat2 written 6 weeks ago by timothyfisher101 • 0 • updated 6 weeks ago by ATpoint ♦ 13k
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Infer experiment - Failed to determine strandin paired end stranded RNA-seq
hisat2 paired end star rna-seq stranded written 11 weeks ago by GiusiG • 0 • updated 9 weeks ago by michael.ante • 3.0k
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How to identify RNA-seq mapped reads to reference genome but not identified by featurecounts of Subread package?
featurecounts rna-seq hisat2 written 11 weeks ago by bk11 • 30 • updated 11 weeks ago by kristoffer.vittingseerup • 1.4k
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How to handle RNASeq reads that can map to both human and mouse ref (e.g. conserved gene regions)?
alignment hisat2 written 11 weeks ago by DVA • 490 • updated 11 weeks ago by JC ♦ 7.4k
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195
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Hisat2 output for stringtie
stringtie hisat2 written 12 weeks ago by Sam • 100 • updated 12 weeks ago by biokoala ♦ 3.6k
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2
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how to extract counts from bam/merge-bam without gtf
R samtools bowtie2 rna-seq hisat2 written 3 months ago by Shahzad • 10 • updated 3 months ago by michael.ante • 3.0k
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1
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hisat2 and RSEM pipeline
software error gtf rna-seq rsem hisat2 written 3 months ago by Shahzad • 10 • updated 3 months ago by EagleEye ♦ 6.2k
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1
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1
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Sorting BAM files from HISAT2 for DEXSeq
dexseq rna-seq hisat2 written 3 months ago by squando • 10 • updated 3 months ago by Ian ♦ 5.3k
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195
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HISAT2 SRR error
srr sra alignment rna-seq hisat2 written 3 months ago by NAVID.BAVI • 0 • updated 3 months ago by genomax ♦ 62k
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485
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1
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HISAT2 Indexing using annotation for Rattus_norvegicus
hisat2 annotation alignment ensembl index written 4 months ago by neranjan • 0
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1
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1
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Is HISAT2 able to output only the best alignment?
hisat2 written 5 months ago by RoseString • 0 • updated 3 months ago by prasundutta87 • 310
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1
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1
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best pipeline to get gene and transcript counts
count alignment star rna-seq hisat2 written 3 months ago by lkianmehr • 30 • updated 3 months ago by t.blasco95 • 30
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5 follow
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To fetch the reads which are being partially mapped to the genome
jvarkit hisat2 star rna-seq bowtie2 written 4 months ago by swadha • 20 • updated 4 months ago by genomax ♦ 62k
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Is TCGA Breast cancer data strand specific?
geneexpression tcga rna-seq strand hisat2 written 4 months ago by Vasu • 300 • updated 4 months ago by genomax ♦ 62k
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Hisat2 alignment results can be ued for TEtoolkit analysis
hisat2 tetoolkit written 4 months ago by lkianmehr • 30 • updated 4 months ago by h.mon ♦ 23k
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Ovation RNA-seq system, bionfomatic alignment and htseq-count
htseq-count rna-seq hisat2 written 4 months ago by nanoide • 10 • updated 4 months ago by caggtaagtat • 420
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1
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1
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Why chromosome coordinates were given for unmapped reads in hisat2?
unmapped alignment rna-seq hisat2 written 4 months ago by xieshaojun0621 • 90
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HISAT2-build killed: 9 macOS
hisat2 build rna-seq index written 4 months ago by datascientist28 • 370
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fastq file do not look as they should (running Hisat2)
fastq rna-seq hisat2 written 4 months ago by luzglongoria • 20
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6 follow
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Compatibility between my reference genome and GTF file
alignment reference genome rna-seq hisat2 written 4 months ago by Batu • 110
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How to bring consistency for genome reference, annotation and index files?
genome annotation rna-seq gencode hisat2 written 4 months ago by Vasu • 300
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6 follow
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hisat2 warning message dunring alignment of fasta file with reference genome
software error next-gen alignment rna-seq hisat2 written 4 months ago by shuksi1984 • 40 • updated 4 months ago by singh.vijender • 30
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