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0
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34
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Variant calling with 5x coverage, human genome
bam samtools alignment snp variant written 7 days ago by Daphnis • 0 • updated 4 days ago by Jennifer Hillman Jackson ♦ 24k
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1
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38
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1
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bam_index_build2() not yet implemented exception on local Galaxy instance - sam-to-bam
bam samtools bam_index_build2() sam written 14 days ago by nhung • 0 • updated 11 days ago by Jennifer Hillman Jackson ♦ 24k
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1
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29
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1
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Filter BAM file by size
bam filter samtools picard written 14 days ago by aparicio2457 • 0 • updated 11 days ago by Jennifer Hillman Jackson ♦ 24k
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52
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Incorrect dependencies used during job run
samtools dependency written 21 days ago by rmse17 • 0
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2
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364
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2
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How to remove soft clipping reads
samtools sam written 7 months ago by Juan Ledesma • 0 • updated 29 days ago by torsten.seemann • 0
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1
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70
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1
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Create and extract consensus sequence after initial genome mapping using a custom genome
assembly samtools galaxy rna-seq written 5 weeks ago by manjunath.keremane • 0 • updated 5 weeks ago by Jennifer Hillman Jackson ♦ 24k
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2
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94
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2
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MPileup SNP and indel caller (Galalxy Version 0.0.1) error
samtools mpileup software error written 7 weeks ago by vanam • 30
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1
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63
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1
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Trouble sorting a BAM file
samtools sort sortsam pca analysis written 10 weeks ago by xpna01t • 0 • updated 10 weeks ago by Jennifer Hillman Jackson ♦ 24k
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1
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65
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1
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SAM-to-BAM; an error occurred setting the metadata for this dataset.
samtools written 10 weeks ago by michael.magnussen.14 • 0 • updated 10 weeks ago by agatyr • 20
2
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1
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214
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1
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samtool sort error in sorting BAM files by read name
bam samtools galaxy software error written 11 weeks ago by egrossi • 0 • updated 11 weeks ago by Jennifer Hillman Jackson ♦ 24k
1
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1
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189
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1
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SAM-to-BAM 'Failed runtime validation of Using reference genome' Error - Local Galaxy instance
bam samtools genome sam index written 12 weeks ago by nhung • 0 • updated 12 weeks ago by Jennifer Hillman Jackson ♦ 24k
2
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1
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93
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1
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Want all counts on MPileup including zero counts
wrapper samtools mpileup tool option written 12 weeks ago by ghalib.bardai • 10 • updated 12 weeks ago by Jennifer Hillman Jackson ♦ 24k
2
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5
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1.3k
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5
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Local Tophat Error "OSError: [Errno 2] No such file or directory"
samtools local admin tophat error written 2.6 years ago by jmnm2201 • 0 • updated 12 weeks ago by yusheng_tan • 0
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2
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1.3k
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2
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Local Tophat Error "OSError: [Errno 2] No such file or directory"
samtools local admin tophat path written 18 months ago by deane • 30 • updated 12 weeks ago by yusheng_tan • 0
4
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1
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148
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1
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Out Of Disk Space with Picard's FastqtoSam Tools from Galaxy
picard galaxy samtools written 3 months ago by mainulhossain • 0 • updated 3 months ago by Bjoern Gruening ♦ 5.0k
2
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1
answer
176
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1
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Filter SAM or BAM: "unknown reference name" when trying to select multiple chromossomes
bam samtools software error aligment written 3 months ago by eurioste • 40 • updated 3 months ago by Jennifer Hillman Jackson ♦ 24k
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1
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89
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1
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Use of slice to estimate rpkm/fpkm
slice samtools rna-seq fpkm/rpkm written 3 months ago by a.morris • 10 • updated 3 months ago by Jennifer Hillman Jackson ♦ 24k
1
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1
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134
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1
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SAM to BAM conversion ERRORS
bam samtools alignment bwa written 3 months ago by amra.dhabalia • 0 • updated 3 months ago by y.hoogstrate • 460
1
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1
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89
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1
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BWA error, dataset conversion, history download questions
dataset samtools history download bwa written 3 months ago by samira.kalayinia • 0 • updated 3 months ago by Jennifer Hillman Jackson ♦ 24k
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3
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298
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3
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Galaxy tool development - how do I get a working samtools?
samtools galaxy written 4 months ago by crashfrog • 0
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1
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146
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1
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Copy/paste single read sequences in excel
samtools galaxy written 5 months ago by a.klausegger • 0 • updated 5 months ago by Jennifer Hillman Jackson ♦ 24k
1
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1
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289
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1
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SAM-to-BAM (NGS: SAMtools)
samtools galaxy written 5 months ago by zli80 • 0 • updated 5 months ago by Devon Ryan • 1.9k
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1
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129
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1
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pileup --position in galaxy
regions samtools pileup mpileup position written 6 months ago by mor.rub • 0 • updated 6 months ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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262
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1
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samtools for 32-bit local galaxy
samtools local path written 6 months ago by harryln • 10 • updated 6 months ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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256
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1
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Extract assembled transcripts from Cufflinks gtf without to use reference genome
bam samtools cufflinks gtf rna-seq written 7 months ago by marija.djurdjevic • 30 • updated 7 months ago by Jennifer Hillman Jackson ♦ 24k
0
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1
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235
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1
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How to extract SNPs from galaxy workflow
samtools galaxy snp alignment written 8 months ago by sureshbabu.angara • 0 • updated 7 months ago by Jennifer Hillman Jackson ♦ 24k
2
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0
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258
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0
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Naive Variant Caller doesn't output variants wile mpileup does
nvc samtools mpileup written 8 months ago by biomonika • 60
0
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2
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354
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2
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MNase ChIP-seq paired-end data analysis ?
chip-seq samtools galaxy bowtie alignment written 8 months ago by ghahhari.nm • 0
3
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5
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1.4k
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5
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Bowtie2 error on locally installed Galaxy : unable to finish job
python bowtie2 oserror path samtools written 2.2 years ago by chaoyuan • 80 • updated 9 months ago by Jennifer Hillman Jackson ♦ 24k
5
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3
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948
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3
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Forum: An entertaining read about BWA, Picard, GATK
galaxy software error forum bwa bam samtools written 13 months ago by apozhitkov • 60 • updated 10 months ago by linying9114 • 0
1
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0
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223
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0
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Sample name on BedCov results
samtools bedcov written 10 months ago by shirley • 10
2
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2
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206
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5 follow
2
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Problem merging five 13.9 GB .BAM files
bam samtools written 10 months ago by rickwhite23 • 10
0
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1
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307
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1
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How to generate pileup file
chip-seq samtools pileup usegalaxy.org usage written 11 months ago by dikshagarg0409 • 0 • updated 11 months ago by Jennifer Hillman Jackson ♦ 24k
4
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1
answer
536
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6 follow
1
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sam to bam - Galaxy version 17.01
galaxy samtools local job-error written 12 months ago by bryan.hepworth • 30 • updated 12 months ago by Jennifer Hillman Jackson ♦ 24k
1
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1
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308
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What Galaxy tools can convert SAM format to the BAM except SAM2BAM which can`t be installed on our instance?
samtools cloud sam2bam installation written 13 months ago by msprindzhuk • 40 • updated 13 months ago by Jennifer Hillman Jackson ♦ 24k
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