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htseq-count error: "does not contain 'gene_id'
htseq-count rna-seq written 4.6 years ago by lynne.m.a.harris • 30 • updated 2 days ago by eennadi • 0
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0
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223
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RNA-Seq, HTSeq-Counts, counts are ~1M less compared to the reference research paper
htseq-count sequence rna-seq written 4 days ago by xytwwwww • 0
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1
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103
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1
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Problem with htseq-count: counts of 0?
genome fasta htseq-count transcriptomics written 5 weeks ago by sbitterw • 0 • updated 5 weeks ago by lieven.sterck ♦ 9.5k
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1
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216
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1
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htseq-count settings for differential expression
htseq-count rna-seq written 11 weeks ago by candron • 10
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1
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156
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1
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problem use htseq-count in bash script
htseq-count script written 8 weeks ago by o.omidan • 10
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139
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Differences between number of expressed genes obtained with RSEM and htseq-count
gene abundance htseq-count rna-seq rsem written 12 weeks ago by concetta • 0
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1
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135
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1
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htseq-count without GTF?
htseq count fpkm htseq-count gtf written 3 months ago by blur • 150 • updated 3 months ago by ATpoint ♦ 44k
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1
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190
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1
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Htseq unable to process last read
htseq-count rna-seq written 4 months ago by Sam • 120
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0
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229
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0
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Counting reads over genes with summarizeOverlaps
htseq-count summarizeoverlaps rna-seq written 6 months ago by concetta • 0
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2
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232
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2
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Merged vs. Ensembl GTF for htseq-count
htseq-count rna-seq written 7 months ago by kousi31 • 30 • updated 7 months ago by kristoffer.vittingseerup • 3.5k
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6 follow
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HTSeq-count in RNA-Seq
htseq-count rna-seq written 2.6 years ago by mlemusfuentes • 10 • updated 10 months ago by Balatheskulter • 0
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1.5k
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Error during htseq-count
htseq-count star pysam written 3.4 years ago by baffiak1902 • 10 • updated 11 months ago by Biostar ♦♦ 20
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3
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htseq-count cannot find pysam
htseq htseq-count quantification rna-seq myposts written 5.1 years ago by Gary • 480 • updated 11 months ago by Payal • 100
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241
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1
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HTseq does not generate any counts file
htseq-count rna-seq written 12 months ago by archisman • 0 • updated 12 months ago by Ido Tamir ♦ 5.1k
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1.1k
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2
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Non-ascii characters in bam file cause htseq-count error
htseq-count star rna-seq written 15 months ago by loui_ • 0 • updated 15 months ago by swbarnes2 ♦ 9.4k
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2
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5 follow
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is 0-based start and 1-based end of bed format not compatible with htseq-count?
index-error 0-based start htseq-count bed to gtf written 16 months ago by Zee_S • 60 • updated 16 months ago by michael.ante • 3.6k
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279
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HT-seq-count default parameter to "score"secondary alignments contradicts its documentation that it ignores multi mappers by default. Not clear!
secondary alignment htseq-count multimapping read written 16 months ago by Zee_S • 60
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332
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Can we make a counting program using GFF3 reference files?
rnaseq htseq-count featurecounts written 17 months ago by ino • 0
6
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2
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903
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2
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Question about exon/intron counting in RNA-seq dataset analysis
htseq-count featurecounts rna-seq written 21 months ago by nanoide • 60 • updated 21 months ago by swbarnes2 ♦ 9.4k
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1
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Ambiguous reads in htseq-count
htseq-count rna-seq written 21 months ago by kousi31 • 30
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1
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641
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1
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how to get gff file bos tau8 from ucsc to import in usegalaxy
gff ucsc htseq-count usegalaxy written 21 months ago by Kian • 40
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1.1k
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5 follow
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FASTQ alignment result is really bad
htseq-count salmon rna-seq written 2.1 years ago by bharata1803 • 490 • updated 2.1 years ago by h.mon ♦ 32k
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1
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1.4k
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1
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STAR quantMode geneCounts: weird outcomes
htseq-count star rna-seq written 2.2 years ago by davide.chiarugi • 20
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823
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Normalization of read counts from HTSeq by library size
R htseq-count deseq2 ngs rna-seq written 2.3 years ago by Susmita Mandal • 70
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1
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816
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1
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Ovation RNA-seq system, bionfomatic alignment and htseq-count
htseq-count rna-seq hisat2 written 2.3 years ago by nanoide • 60 • updated 2.3 years ago by caggtaagtat • 1.4k
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1.7k
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1
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Malformed SAM line error with HTSeq
htseq-count written 4.9 years ago by Kssr • 110 • updated 2.3 years ago by _r_am ♦ 32k
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1.8k
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featurecounts more fragments than input read pairs
htseq-count featurecounts pair-end rna-seq written 2.5 years ago by ewre • 220 • updated 2.3 years ago by Biostar ♦♦ 20
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Htseq: High number of no_feature
htseq-count rna-seq written 2.4 years ago by nadja.g • 0 • updated 2.4 years ago by GenoMax ♦ 94k
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Salmon quantification vs HTSeq count quantification
htseq-count salmon written 2.4 years ago by pablo • 150 • updated 2.4 years ago by h.mon ♦ 32k
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Preprocessing for DESeq2 - create metadata table
htseq-count deseq2 rna-seq written 2.4 years ago by alexadeanfitz • 10 • updated 2.4 years ago by h.mon ♦ 32k
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