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BAM tool?? tab-delimited, coordinate sorted output file - displays calls, depth at every coordinate?
bam samtools written 3 days ago by zhalford • 0
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2
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86
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2
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Interpreting detected "duplicates" between different tools
galaxy samtools fastqc bwa picard written 4 weeks ago by joseludenia • 0
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1
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57
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1
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Regarding reads extract from bam file
bamfile bam galaxy mapping samtools written 27 days ago by DL • 0 • updated 27 days ago by Jennifer Hillman Jackson ♦ 25k
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2
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673
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2
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How to access datacollection metadata (input names of elements)
samtools tool development metadata data collection written 23 months ago by fiebig • 30 • updated 5 weeks ago by bio.erikson • 0
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3
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281
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3
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Ubuntu 18.04. Samtools missing tool dependencies
ncurses 5.9 samtools galaxy admin ubuntu written 11 weeks ago by alexshakhin • 0
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1
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122
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1
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Extract aligned exactly 1 time fron Bowtie2?
samtools bowtie2 galaxy alignment written 3 months ago by star • 0 • updated 3 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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103
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1
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Understanding and decoding SAM or BAM flags
bam samtools flag bamcoverage sam written 3 months ago by jailyn.han • 10 • updated 3 months ago by Jennifer Hillman Jackson ♦ 25k
2
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1
answer
144
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1
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multi bam summary
chip-seq bam error sort samtools written 3 months ago by lnaren • 10 • updated 3 months ago by Jennifer Hillman Jackson ♦ 25k
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2
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120
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2
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galaxy_filter_sam report error
bam samtools galaxy sort picard written 3 months ago by garentguuu • 10
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1
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126
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1
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Variant calling with 5x coverage, human genome
bam samtools alignment snp variant written 4 months ago by Daphnis • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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138
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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 4 months ago by nhung • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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159
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1
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Filter BAM file by size
bam filter samtools picard written 4 months ago by aparicio2457 • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 25k
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197
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Incorrect dependencies used during job run
samtools dependency written 4 months ago by rmse17 • 0
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2
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610
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2
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How to remove soft clipping reads
samtools sam written 11 months ago by Juan Ledesma • 0 • updated 5 months ago by torsten.seemann • 0
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1
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406
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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 months ago by manjunath.keremane • 0 • updated 5 months ago by Jennifer Hillman Jackson ♦ 25k
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2
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248
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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 5 months ago by vanam • 30
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1
answer
180
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1
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Trouble sorting a BAM file
samtools sort sortsam pca analysis written 6 months ago by xpna01t • 0 • updated 6 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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176
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1
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SAM-to-BAM; an error occurred setting the metadata for this dataset.
samtools written 6 months ago by michael.magnussen.14 • 0 • updated 6 months ago by agatyr • 20
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1
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513
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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 6 months ago by egrossi • 0 • updated 6 months ago by Jennifer Hillman Jackson ♦ 25k
1
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1
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306
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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 7 months ago by nhung • 0 • updated 6 months ago by Jennifer Hillman Jackson ♦ 25k
2
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1
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170
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1
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Want all counts on MPileup including zero counts
wrapper samtools mpileup tool option written 6 months ago by ghalib.bardai • 10 • updated 6 months ago by Jennifer Hillman Jackson ♦ 25k
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5
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1.5k
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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 2.9 years ago by jmnm2201 • 0 • updated 7 months ago by yusheng_tan • 0
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2
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1.6k
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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 22 months ago by deane • 30 • updated 7 months ago by yusheng_tan • 0
4
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1
answer
299
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1
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Out Of Disk Space with Picard's FastqtoSam Tools from Galaxy
picard galaxy samtools written 7 months ago by mainulhossain • 0 • updated 7 months ago by Bjoern Gruening ♦ 5.1k
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1
answer
398
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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 7 months ago by eurioste • 40 • updated 7 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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234
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1
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Use of slice to estimate rpkm/fpkm
slice samtools rna-seq fpkm/rpkm written 7 months ago by a.morris • 40 • updated 7 months ago by Jennifer Hillman Jackson ♦ 25k
1
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1
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344
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1
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SAM to BAM conversion ERRORS
bam samtools alignment bwa written 7 months ago by amra.dhabalia • 0 • updated 7 months ago by y.hoogstrate • 460
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1
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179
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1
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BWA error, dataset conversion, history download questions
dataset samtools history download bwa written 7 months ago by samira.kalayinia • 0 • updated 7 months ago by Jennifer Hillman Jackson ♦ 25k
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3
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444
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3
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Galaxy tool development - how do I get a working samtools?
samtools galaxy written 8 months ago by crashfrog • 0
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1
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275
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1
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Copy/paste single read sequences in excel
samtools galaxy written 9 months ago by a.klausegger • 0 • updated 9 months ago by Jennifer Hillman Jackson ♦ 25k
1
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1
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428
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1
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SAM-to-BAM (NGS: SAMtools)
samtools galaxy written 9 months ago by zli80 • 0 • updated 9 months ago by Devon Ryan • 1.9k
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1
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198
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1
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pileup --position in galaxy
regions samtools pileup mpileup position written 10 months ago by mor.rub • 0 • updated 10 months ago by Jennifer Hillman Jackson ♦ 25k
0
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1
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385
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1
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samtools for 32-bit local galaxy
samtools local path written 10 months ago by harryln • 10 • updated 10 months ago by Jennifer Hillman Jackson ♦ 25k
0
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1
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380
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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 11 months ago by marija.djurdjevic • 30 • updated 11 months ago by Jennifer Hillman Jackson ♦ 25k
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1
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373
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1
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How to extract SNPs from galaxy workflow
samtools galaxy snp alignment written 12 months ago by sureshbabu.angara • 0 • updated 11 months ago by Jennifer Hillman Jackson ♦ 25k
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