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<prev • 118 results • page 1 of 4 • next >
0
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Stringtie elimination of important transcripts
assembly stringtie alignment rna-seq hisat2 written 15 hours ago by ra2967 • 10 • updated 12 hours ago by manuel.belmadani • 70
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1
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79
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1
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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 days ago by O.rka • 70 • updated 5 days ago by swbarnes2 ♦ 4.7k
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158
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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 14 days ago by timothyfisher101 • 0 • updated 13 days ago by ATpoint ♦ 12k
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1
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136
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1
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Infer experiment - Failed to determine strandin paired end stranded RNA-seq
hisat2 paired end star rna-seq stranded written 7 weeks ago by GiusiG • 0 • updated 4 weeks ago by michael.ante • 2.9k
2
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1
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188
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1
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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 6 weeks ago by bk11 • 30 • updated 6 weeks ago by kristoffer.vittingseerup • 1.2k
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1
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103
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1
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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 7 weeks ago by DVA • 480 • updated 7 weeks ago by JC ♦ 7.1k
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1
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155
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1
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Hisat2 output for stringtie
stringtie hisat2 written 7 weeks ago by Sam • 80 • updated 7 weeks ago by Vijay Lakhujani ♦ 3.5k
3
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2
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167
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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 10 weeks ago by Shahzad • 10 • updated 10 weeks ago by michael.ante • 2.9k
0
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1
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207
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1
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hisat2 and RSEM pipeline
software error gtf rna-seq rsem hisat2 written 10 weeks ago by Shahzad • 10 • updated 10 weeks ago by EagleEye ♦ 6.1k
2
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1
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216
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1
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Sorting BAM files from HISAT2 for DEXSeq
dexseq rna-seq hisat2 written 11 weeks ago by squando • 10 • updated 10 weeks ago by Ian ♦ 5.3k
1
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157
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0
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HISAT2 SRR error
srr sra alignment rna-seq hisat2 written 11 weeks ago by NAVID.BAVI • 0 • updated 11 weeks ago by genomax ♦ 60k
5
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1
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407
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1
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HISAT2 Indexing using annotation for Rattus_norvegicus
hisat2 annotation alignment ensembl index written 12 weeks ago by neranjan • 0
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1
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262
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1
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Is HISAT2 able to output only the best alignment?
hisat2 written 4 months ago by RoseString • 0 • updated 12 weeks ago by prasundutta87 • 300
3
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1
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341
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1
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best pipeline to get gene and transcript counts
count alignment star rna-seq hisat2 written 12 weeks ago by lkianmehr • 30 • updated 12 weeks ago by t.blasco95 • 30
1
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0
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168
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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 3 months ago by swadha • 20 • updated 3 months ago by genomax ♦ 60k
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1
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250
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1
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Is TCGA Breast cancer data strand specific?
geneexpression tcga rna-seq strand hisat2 written 3 months ago by Bioinfo • 270 • updated 3 months ago by genomax ♦ 60k
1
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1
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131
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1
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Hisat2 alignment results can be ued for TEtoolkit analysis
hisat2 tetoolkit written 3 months ago by lkianmehr • 30 • updated 3 months ago by h.mon ♦ 22k
5
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1
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230
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1
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Ovation RNA-seq system, bionfomatic alignment and htseq-count
htseq-count rna-seq hisat2 written 3 months ago by nanoide • 10 • updated 3 months ago by caggtaagtat • 390
2
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1
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156
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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 3 months ago by xieshaojun0621 • 90
1
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1
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185
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1
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HISAT2-build killed: 9 macOS
hisat2 build rna-seq index written 3 months ago by datascientist28 • 350
2
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1
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294
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1
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fastq file do not look as they should (running Hisat2)
fastq rna-seq hisat2 written 3 months ago by luzglongoria • 0
6
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0
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311
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6 follow
0
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Compatibility between my reference genome and GTF file
alignment reference genome rna-seq hisat2 written 3 months ago by Batu • 110
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280
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0
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How to bring consistency for genome reference, annotation and index files?
genome annotation rna-seq gencode hisat2 written 3 months ago by Bioinfo • 270
8
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1
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366
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6 follow
1
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hisat2 warning message dunring alignment of fasta file with reference genome
software error next-gen alignment rna-seq hisat2 written 3 months ago by shuksi1984 • 40 • updated 3 months ago by singh.vijender • 20
2
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1
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190
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1
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How to deal with single transcripts assigned to multiple genes?
stringtie rna-seq hisat2 written 3 months ago by antoinefelden • 20 • updated 3 months ago by RamRS ♦ 20k
2
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1
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404
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1
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hisat2 / bowtie: read has more quality values than read characters
bowtie2 hisat2 bowtie hisat written 4 months ago by juan.crescente • 20
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2
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246
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5 follow
2
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Proper design for DESeq2 and other RNAseq general questions
stringtie deseq2 rna-seq hisat2 written 3 months ago by Stef • 0 • updated 3 months ago by swbarnes2 ♦ 4.7k
6
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1
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314
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1
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Problem mapping with STAR
tophat star hisat2 written 4 months ago by alvarocentron91 • 0 • updated 4 months ago by WouterDeCoster ♦ 35k
1
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0
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255
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0
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Prepare multiple gtf files for Ballgown
hisat rna-seq hisat2 written 4 months ago by catglen012 • 0
0
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235
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0
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Advantage of making HISAT2 genome index with annotation file
reference index annotations hisat2 written 4 months ago by piyushjo • 100 • updated 4 months ago by RamRS ♦ 20k
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