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Troubleshooting: Problem TopHat paired data
hisat2 galaxy tophat rna-seq written 6 days ago by Jonathan.Burghofer • 0 • updated 6 days ago by Jennifer Hillman Jackson ♦ 25k
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1
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38
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1
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TopHat Align Summary - whats a good results
hisat2 mapping tophat rna-seq written 9 days ago by mbt • 0 • updated 9 days ago by Jennifer Hillman Jackson ♦ 25k
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1
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44
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1
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How I can to remove specific sequence from a fungu of a plant-fungu interaction of total RNA-Seq data?
hisat2 galaxy rna-seq written 20 days ago by uli.arcos8 • 0 • updated 20 days ago by Jennifer Hillman Jackson ♦ 25k
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1
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50
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1
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HISAT2 Output in Galaxy vs Command Line
hisat2 bam galaxy sort coordinate written 28 days ago by sdbaney • 10 • updated 28 days ago by Jennifer Hillman Jackson ♦ 25k
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149
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Filtering BAM files from HISAT2
bam hisat2 alignment rna-seq written 8 weeks ago by dexter.myrick • 30 • updated 8 weeks ago by Jennifer Hillman Jackson ♦ 25k
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2
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145
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2
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HISAT2 and Rat annotation database
hisat2 annotation gtf rna-seq written 3 months ago by andrewzlobin • 20
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1
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167
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1
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RNA-STAR Failing using hg38 but works for hg19
hisat2 rna-seq usage memory star written 3 months ago by aklie • 0 • updated 3 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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183
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1
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Query for inputting Hisat2 BAM with dataset collections for Stringtie analysis
quota hisat2 rna-seq job stringtie written 3 months ago by pravikumar • 0 • updated 3 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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141
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1
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Galaxy shows error while running tophat (deprecated tool, use HISAT2 instead)
deprecated hisat2 galaxy tophat rna-seq written 3 months ago by kudzu • 10 • updated 3 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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432
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1
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Featurecounts for paired end RNA-seq reads not generating counts
hisat2 featurecounts rna-seq written 4 months ago by skumar53 • 30 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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207
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1
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RNA STAR and HISAT2 job errors (memory failures)
hisat2 rna-seq star memory error written 4 months ago by theodorcrispin • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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222
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1
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RNA STAR error
rna star hisat2 memory-error star written 4 months ago by theodorcrispin • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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2
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181
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2
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HISAT2 output error
hisat2 rna-seq written 4 months ago by carrollc2 • 0
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1
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296
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1
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Samtools error assoicated with multiple mapping tools
hisat2 galaxy bwa written 4 months ago by gkuffel22 • 170 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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212
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1
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Hitsat2: Spliced alignment options
hisat2 galaxy gtf annotation rna-seq written 4 months ago by audrey.mohr • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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475
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1
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Error running cufflinks ( found spliced alignment without XS attribute) when use HISAT2 output Bam file
hisat2 cufflinks galaxy written 4 months ago by fat2008vet • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
2
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1
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191
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1
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Top Hat deprecation--what should I use?
hisat2 mapping star tophat rna-seq written 4 months ago by sadequr.rahman • 10 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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155
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1
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Problem with Hisat2
bam hisat2 alignment rna-seq written 4 months ago by rptiluswatson • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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165
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1
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Job Submission Failed
hisat2 input salmon software error rna-seq written 5 months ago by cjmoor2 • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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251
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1
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Non-coding RNA feature type/attribute
hisat2 htseq-count attribute gff3 htseq written 5 months ago by exd5048 • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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2
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262
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2
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why TopHat doesn't read my compressed dataset collection (Fastqsanger.gz)? -- Deprecated tool, use HISAT2 instead
hisat2 collection galaxy fastqsangergz tophat written 5 months ago by Fat.eldefrawy • 10
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227
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unable to load zebrafish GTF/GFF3 files from current history into any of the RNA analysis tools
hisat2 gtf star tophat rna-seq written 5 months ago by goreaniket • 0 • updated 5 months ago by Jennifer Hillman Jackson ♦ 25k
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233
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A tool is marked deprecated, should I use it?
hisat2 tutorials tophat queue rna-seq written 5 months ago by theodorcrispin • 0 • updated 5 months ago by jevanveen • 10
2
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1
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162
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1
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Empty data result from Cufflinks
hisat2 custom cufflinks gtf genome written 5 months ago by a.walne • 40 • updated 5 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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217
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1
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HISAT2 soft clipping
hisat2 usegalaxy.org 2.1.0 software error written 5 months ago by hermane • 0 • updated 5 months ago by Jennifer Hillman Jackson ♦ 25k
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444
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1
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How to prepare FastQ files for HISAT2
hisat2 rna-seq alignment fastq written 6 months ago by skhan • 40 • updated 6 months ago by Jennifer Hillman Jackson ♦ 25k
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456
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HISAT2 input to StringTie with converted GFF > GTF produces error message
hisat2 stringtie gtf gff3 gff written 6 months ago by ramibalasubramanian • 0 • updated 6 months ago by Jennifer Hillman Jackson ♦ 25k
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442
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HISAT2 input to StringTie with UCSC mm10 or ncbi refseq GTF produces error message
hisat2 stringtie annotation gtf rna-seq written 6 months ago by gozrom • 0 • updated 6 months ago by Jennifer Hillman Jackson ♦ 25k
0
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1
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217
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1
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Problem with Reference genome from history in Tuxedo
hisat2 custom-genome tophat2 queue rna-seq written 7 months ago by vsafavi • 0 • updated 7 months ago by Jennifer Hillman Jackson ♦ 25k
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222
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1
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HISAT2/TOPHAT alignment to a Rabbit Genome
hisat2 rabbit alignment tophat written 7 months ago by deemergd92 • 0 • updated 7 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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308
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1
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BAM file problems, sorting filtering and running naive variant called
nvc hisat2 freebayes variant rna-seq written 7 months ago by keeley.brookes • 0 • updated 7 months ago by Jennifer Hillman Jackson ♦ 25k
0
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229
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Error: Remote job server indicated a problem running or monitoring this job
hisat2 tophat software error tophat2 rna-seq written 7 months ago by kelly.hudspeth • 0 • updated 7 months ago by Jennifer Hillman Jackson ♦ 25k
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267
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Matched error with cuffdiff
cuffdiff hisat2 galaxy rna-seq error written 9 months ago by annet.kyomuhangi • 10 • updated 9 months ago by Jennifer Hillman Jackson ♦ 25k
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2
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288
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RNA-Seq Alignment too Big for Galaxy?
hisat2 rnastar rna-seq star hisat written 9 months ago by Newbie • 0 • updated 9 months ago by Jennifer Hillman Jackson ♦ 25k
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variable, low alignment rates with HISAT2
hisat2 alignment rna-seq written 9 months ago by stephanie.major • 10 • updated 9 months ago by ellascottgm • 0
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