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0
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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 1 day ago by goreaniket • 0 • updated 1 day ago by Jennifer Hillman Jackson ♦ 24k
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1
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27
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1
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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 2 days ago by Fat.eldefrawy • 0 • updated 1 day ago by Jennifer Hillman Jackson ♦ 24k
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2
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43
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2
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A tool is marked deprecated, should I use it?
hisat2 tutorials tophat queue rna-seq written 8 days ago by theodorcrispin • 0 • updated 7 days ago by jevanveen • 10
2
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1
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49
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1
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Empty data result from Cufflinks
hisat2 custom cufflinks gtf genome written 25 days ago by a.walne • 20 • updated 24 days ago by Jennifer Hillman Jackson ♦ 24k
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1
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61
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1
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HISAT2 soft clipping
hisat2 usegalaxy.org 2.1.0 software error written 26 days ago by hermane • 0 • updated 25 days ago by Jennifer Hillman Jackson ♦ 24k
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1
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93
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1
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How to prepare FastQ files for HISAT2
hisat2 rna-seq alignment fastq written 6 weeks ago by skhan • 30 • updated 6 weeks ago by Jennifer Hillman Jackson ♦ 24k
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1
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84
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1
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HISAT2 input to StringTie with converted GFF > GTF produces error message
hisat2 stringtie gtf gff3 gff written 7 weeks ago by ramibalasubramanian • 0 • updated 7 weeks ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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116
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1
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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 7 weeks ago by gozrom • 0 • updated 7 weeks ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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64
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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 8 weeks ago by vsafavi • 0 • updated 8 weeks ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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69
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1
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HISAT2/TOPHAT alignment to a Rabbit Genome
hisat2 rabbit alignment tophat written 10 weeks ago by deemergd92 • 0 • updated 10 weeks ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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170
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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 11 weeks ago by keeley.brookes • 0 • updated 11 weeks ago by Jennifer Hillman Jackson ♦ 24k
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1
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98
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1
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Error: Remote job server indicated a problem running or monitoring this job
hisat2 tophat software error tophat2 rna-seq written 11 weeks ago by kelly.hudspeth • 0 • updated 11 weeks ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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151
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1
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Matched error with cuffdiff
cuffdiff hisat2 galaxy rna-seq error written 4 months ago by annet.kyomuhangi • 10 • updated 4 months ago by Jennifer Hillman Jackson ♦ 24k
1
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2
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152
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2
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RNA-Seq Alignment too Big for Galaxy?
hisat2 rnastar rna-seq star hisat written 4 months ago by Newbie • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 24k
1
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2
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362
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2
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variable, low alignment rates with HISAT2
hisat2 alignment rna-seq written 4 months ago by stephanie.major • 10 • updated 4 months ago by ellascottgm • 0
0
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1
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269
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1
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Stringtie Deseq2/EdgeR count tables all zero
hisat2 stringtie rna-seq deseq2 written 4 months ago by scholtz • 60 • updated 4 months ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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209
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1
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RNA Star: Problem with tool
hisat2 rnastar galaxy tophat rna-seq written 5 months ago by wcheng • 10 • updated 5 months ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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177
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1
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Job execution delays due to input dataset states
hisat2 metadata jobs tophat queue written 5 months ago by lippsdd • 0 • updated 5 months ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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211
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1
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RNA STAR job error
hisat2 input rna-seq job error written 5 months ago by k.makwana • 20 • updated 5 months ago by Jennifer Hillman Jackson ♦ 24k
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1
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349
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1
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Which reference to map against for RNA-Seq using HISAT2
hisat2 rna-seq written 5 months ago by skhan • 30 • updated 5 months ago by Jennifer Hillman Jackson ♦ 24k
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3
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642
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3
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HiSAT2 Alignment Rate Dropping with Cufflinks export option enabled
hisat2 cufflinks rna-seq written 12 months ago by nick.andrews15 • 0 • updated 6 months ago by Widmer, Giovanni • 150
0
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1
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163
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1
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HISAT2 job not running
hisat2 rna-seq written 9 months ago by s1532897 • 0 • updated 9 months ago by Jennifer Hillman Jackson ♦ 24k
1
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1
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353
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1
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HISAT2: "Skip reference strand of reference" instead of "Skip REVERSE strand of reference"
hisat2 name galaxy parameter written 9 months ago by aciole.d • 0 • updated 9 months ago by Jennifer Hillman Jackson ♦ 24k
1
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1
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554
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1
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HISAT2 gzip: input_r.fastq.gz: not in gzip format
hisat2 gzip rna-seq written 10 months ago by testtoolshed • 30 • updated 10 months ago by Jennifer Hillman Jackson ♦ 24k
1
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1
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474
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1
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instructions for fetching and install mm10 genome and hisat indexing for local galaxy
hisat2 index refererence genome written 14 months ago by vaughandy • 10 • updated 14 months ago by Jennifer Hillman Jackson ♦ 24k
1
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0
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0
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hisat2 index issue (I think)
hisat2 index hisat reference genome written 14 months ago by vaughandy • 10
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2
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560
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2
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HISAT2 path problem (I think)
hisat2 samtools ubuntu path written 14 months ago by vaughandy • 10 • updated 14 months ago by Jennifer Hillman Jackson ♦ 24k
1
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1
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882
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1
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Hisat2 Cufflinks Cuffmerge cuffdiff problems
hisat2 rna-seq cufflinks cuffmerge cuffdif written 19 months ago by vm.higareda • 0 • updated 19 months ago by Jennifer Hillman Jackson ♦ 24k
2
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1
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818
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1
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Cuffquant errors after using HISAT2
cuffquant hisat2 cufflinks galaxy rna-seq written 22 months ago by ali.saberi92 • 0 • updated 22 months ago by rkp21 • 20
0
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1
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621
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1
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HiSat2: 24 hours later, status gray and says: "This is a new dataset and not all of its data are available yet"
hisat2 written 24 months ago by becky.mackelprang • 0 • updated 24 months ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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808
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1
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built-in genome for HISAT2 not available
hisat2 indexes genome written 2.1 years ago by jchou • 0 • updated 2.1 years ago by Jennifer Hillman Jackson ♦ 24k
3
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2
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742
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2
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Is HISAT2 working in GALAXY?
hisat2 galaxy written 2.2 years ago by cooleel • 0
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