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0
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1
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15
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1
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Bowtie2/Samtools files are not visualized with Trackster: Fatal error Exit code 255 ()
bam samtools sam bowtie trackster written 2 days ago by jrzupan • 0 • updated 2 days ago by Jennifer Hillman Jackson ♦ 25k
0
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1
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85
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1
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mpileup warning and problem with bcftools call
samtools written 26 days ago by aymeric.goyer • 0 • updated 25 days ago by Jennifer Hillman Jackson ♦ 25k
3
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2
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99
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2
answers
Iterative Mapping -> open: No such file or directory
samtools galaxy iterative mapping output written 7 weeks ago by stoyan.velkov • 10
0
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2
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80
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2
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SamToFastq: SAM validation error
samtools galaxy written 7 weeks ago by lim.michelle.25 • 0
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1
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86
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1
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BAM tool?? tab-delimited, coordinate sorted output file - displays calls, depth at every coordinate?
bam samtools written 8 weeks ago by zhalford • 0 • updated 8 weeks ago by Jennifer Hillman Jackson ♦ 25k
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2
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187
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2
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Interpreting detected "duplicates" between different tools
galaxy samtools fastqc bwa picard written 12 weeks ago by julieta • 0
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1
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108
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1
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Regarding reads extract from bam file
bamfile bam galaxy mapping samtools written 12 weeks ago by DL • 0 • updated 12 weeks ago by Jennifer Hillman Jackson ♦ 25k
1
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2
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782
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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 2.1 years ago by fiebig • 30 • updated 3 months ago by bio.erikson • 0
1
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3
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383
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3
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Ubuntu 18.04. Samtools missing tool dependencies
ncurses 5.9 samtools galaxy admin ubuntu written 4 months ago by alexshakhin • 0
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1
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243
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1
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Extract aligned exactly 1 time fron Bowtie2?
samtools bowtie2 galaxy alignment written 5 months ago by star • 0 • updated 5 months ago by Jennifer Hillman Jackson ♦ 25k
1
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1
answer
170
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1
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Understanding and decoding SAM or BAM flags
bam samtools flag bamcoverage sam written 5 months ago by jailyn.han • 10 • updated 5 months ago by Jennifer Hillman Jackson ♦ 25k
2
votes
1
answer
212
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1
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multi bam summary
chip-seq bam error sort samtools written 5 months ago by lnaren • 10 • updated 5 months ago by Jennifer Hillman Jackson ♦ 25k
0
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2
answers
197
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2
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galaxy_filter_sam report error
bam samtools galaxy sort picard written 5 months ago by garentguuu • 10
0
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1
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173
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1
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Variant calling with 5x coverage, human genome
bam samtools alignment snp variant written 6 months ago by Daphnis • 0 • updated 6 months ago by Jennifer Hillman Jackson ♦ 25k
0
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1
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180
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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 6 months ago by nhung • 10 • updated 6 months ago by Jennifer Hillman Jackson ♦ 25k
0
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1
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255
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1
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Filter BAM file by size
bam filter samtools picard written 6 months ago by aparicio2457 • 0 • updated 6 months ago by Jennifer Hillman Jackson ♦ 25k
0
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0
answers
302
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0
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Incorrect dependencies used during job run
samtools dependency written 6 months ago by rmse17 • 0
0
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2
answers
782
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2
answers
How to remove soft clipping reads
samtools sam written 13 months ago by Juan Ledesma • 0 • updated 6 months ago by torsten.seemann • 0
0
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1
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546
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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 7 months ago by manjunath.keremane • 0 • updated 7 months ago by Jennifer Hillman Jackson ♦ 25k
1
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2
answers
325
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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 months ago by vanam • 30
0
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1
answer
239
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1
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Trouble sorting a BAM file
samtools sort sortsam pca analysis written 8 months ago by xpna01t • 0 • updated 8 months ago by Jennifer Hillman Jackson ♦ 25k
0
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1
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230
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1
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SAM-to-BAM; an error occurred setting the metadata for this dataset.
samtools written 8 months ago by michael.magnussen.14 • 0 • updated 8 months ago by agatyr • 20
2
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1
answer
689
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1
answer
samtool sort error in sorting BAM files by read name
bam samtools galaxy software error written 8 months ago by egrossi • 0 • updated 8 months ago by Jennifer Hillman Jackson ♦ 25k
2
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1
answer
422
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1
answer
SAM-to-BAM 'Failed runtime validation of Using reference genome' Error - Local Galaxy instance
bam samtools genome sam index written 8 months ago by nhung • 10 • updated 8 months ago by Jennifer Hillman Jackson ♦ 25k
2
votes
1
answer
211
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1
answer
Want all counts on MPileup including zero counts
wrapper samtools mpileup tool option written 8 months ago by ghalib.bardai • 10 • updated 8 months ago by Jennifer Hillman Jackson ♦ 25k
2
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5
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1.7k
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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 3.1 years ago by jmnm2201 • 0 • updated 8 months ago by yusheng_tan • 0
3
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2
answers
1.8k
views
2
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Local Tophat Error "OSError: [Errno 2] No such file or directory"
samtools local admin tophat path written 24 months ago by deane • 30 • updated 8 months ago by yusheng_tan • 0
4
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1
answer
386
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1
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Out Of Disk Space with Picard's FastqtoSam Tools from Galaxy
picard galaxy samtools written 9 months ago by mainulhossain • 0 • updated 8 months ago by Bjoern Gruening ♦ 5.1k
2
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1
answer
504
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1
answer
Filter SAM or BAM: "unknown reference name" when trying to select multiple chromossomes
bam samtools software error aligment written 9 months ago by eurioste • 40 • updated 9 months ago by Jennifer Hillman Jackson ♦ 25k
0
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1
answer
281
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1
answer
Use of slice to estimate rpkm/fpkm
slice samtools rna-seq fpkm/rpkm written 9 months ago by a.morris • 40 • updated 9 months ago by Jennifer Hillman Jackson ♦ 25k
1
vote
1
answer
478
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1
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SAM to BAM conversion ERRORS
bam samtools alignment bwa written 9 months ago by amra.dhabalia • 0 • updated 9 months ago by y.hoogstrate • 460
1
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1
answer
248
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1
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BWA error, dataset conversion, history download questions
dataset samtools history download bwa written 9 months ago by samira.kalayinia • 0 • updated 9 months ago by Jennifer Hillman Jackson ♦ 25k
0
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3
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548
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3
answers
Galaxy tool development - how do I get a working samtools?
samtools galaxy written 10 months ago by crashfrog • 0
0
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1
answer
334
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1
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Copy/paste single read sequences in excel
samtools galaxy written 11 months ago by a.klausegger • 0 • updated 11 months ago by Jennifer Hillman Jackson ♦ 25k
1
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1
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488
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1
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SAM-to-BAM (NGS: SAMtools)
samtools galaxy written 11 months ago by zli80 • 0 • updated 11 months ago by Devon Ryan • 1.9k
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