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How to extract SNPs from galaxy workflow
samtools galaxy snp alignment written 3 hours ago by sureshbabu.angara • 0
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2
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45
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2
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MNase ChIP-seq paired-end data analysis ?
chip-seq samtools galaxy bowtie alignment written 12 days ago by ghahhari.nm • 0
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3
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429
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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 5 months ago by apozhitkov • 40 • updated 8 weeks ago by linying9114 • 0
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50
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Sample name on BedCov results
samtools bedcov written 9 weeks ago by shirley • 10
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2
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66
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5 follow
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Problem merging five 13.9 GB .BAM files
bam samtools written 10 weeks ago by rickwhite23 • 10
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1
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110
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1
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How to generate pileup file
chip-seq samtools pileup usegalaxy.org usage written 3 months ago by dikshagarg0409 • 0 • updated 3 months ago by Jennifer Hillman Jackson ♦ 22k
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198
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6 follow
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sam to bam - Galaxy version 17.01
galaxy samtools local job-error written 3 months ago by bryan.hepworth • 30 • updated 3 months ago by Jennifer Hillman Jackson ♦ 22k
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146
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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 5 months ago by msprindzhuk • 40 • updated 5 months ago by Jennifer Hillman Jackson ♦ 22k
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161
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Sam To Bam tool hangs in Cloning stage, though other tools, including Pilon, could be installed
samtools sam2bam written 5 months ago by msprindzhuk • 40 • updated 5 months ago by Jennifer Hillman Jackson ♦ 22k
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249
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Removing sequence duplicates
samtools bowtie tophat written 5 months ago by msumaira36 • 0
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1
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443
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1
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Interpreting Stats output of SAM tools
chip-seq samtools bam written 5 months ago by hpremathilake • 20 • updated 5 months ago by Jennifer Hillman Jackson ♦ 22k
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1
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224
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1
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MAF to VCF showing Indels and snps
samtools alignment written 6 months ago by kmurph55 • 0 • updated 6 months ago by Jennifer Hillman Jackson ♦ 22k
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3
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209
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5 follow
3
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Flow issues? (no temp SAM/BAM to start run?)
bam samtools usegalaxy.org workflow written 8 months ago by dragon28 • 30
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1
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214
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Can't do sam to bam conversion
samtools bowtie snp written 8 months ago by tanvee • 0 • updated 8 months ago by Jennifer Hillman Jackson ♦ 22k
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3
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281
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3
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Mapping using multiple reference sequences
reference mapping samtools bwa bam written 9 months ago by Juan Ledesma • 0
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1
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495
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1
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Trying to understand the steps for 'identify DNA polymorphism sites'
bam samtools galaxy snp bwa written 9 months ago by pilargomez91 • 0 • updated 9 months ago by Jennifer Hillman Jackson ♦ 22k
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1
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241
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1
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Upload Jatropha Reference genome for Bowtie2
samtools galaxy bowtie alignment bwa written 9 months ago by anoopanandmalik • 0 • updated 9 months ago by Jennifer Hillman Jackson ♦ 22k
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701
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2
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Local Tophat Error "OSError: [Errno 2] No such file or directory"
samtools local software error tophat admin written 10 months ago by deane • 20 • updated 10 months ago by Jennifer Hillman Jackson ♦ 22k
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5
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814
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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 23 months ago by jmnm2201 • 0 • updated 10 months ago by Jennifer Hillman Jackson ♦ 22k
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2
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535
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HISAT2 "OSError: [Errno 2] No such file or directory" (Samtools install problem on a local Galaxy)
samtools local error admin hisat written 10 months ago by djevo1 • 40 • updated 10 months ago by Jennifer Hillman Jackson ♦ 22k
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348
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1
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'BEDcov' and 'compute depth and breadth'
bam samtools coverage bed bedtools written 10 months ago by c.zijlstra • 0 • updated 10 months ago by Jennifer Hillman Jackson ♦ 22k
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1
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355
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1
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Error: "Samtools not found" on a local Galaxy when running other jobs
samtools local galaxy hisat rna-seq written 10 months ago by djevo1 • 40 • updated 10 months ago by Jennifer Hillman Jackson ♦ 22k
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1
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263
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1
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Low data conversion rate for BAM-to-SAM. Fix Database, Datatype, Sorting
bam samtools database datatype fastq written 10 months ago by cwalker912 • 0 • updated 10 months ago by Jennifer Hillman Jackson ♦ 22k
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6
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529
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6
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Bam File error uploading
samtools error admin path upload written 11 months ago by shambyross • 10 • updated 10 months ago by y.hoogstrate • 440
2
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2
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350
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2
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No space left on device error (filezilla and processing jobs)
chip-seq samtools galaxy software error bwa written 10 months ago by k.vanduijvenboden • 30 • updated 10 months ago by a.turtoi • 50
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1
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437
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1
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mpileup error: reference sequence is not being fetched correctly?
samtools mpileup reference genome dbkey written 10 months ago by mkim3 • 10 • updated 10 months ago by Jennifer Hillman Jackson ♦ 22k
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1
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310
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1
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How to access datacollection metadata (input names of elements)
samtools tool development metadata data collection written 11 months ago by fiebig • 30
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239
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Missing genome for SAM-to-BAM conversion
samtools database metadata tool input written 11 months ago by nicholas.anthony • 0 • updated 11 months ago by Jennifer Hillman Jackson ♦ 22k
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290
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0
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Cuffdiff Error- empty output files URGENT
samtools cufflinks rna-seq written 12 months ago by Lindsay44 • 0
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0
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342
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0
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Tutorial: Sorted inputs and unexpected results or errors
rna-seq picard gtf tutorial bam samtools written 13 months ago by Jennifer Hillman Jackson ♦ 22k
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1
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RNA-seq analysis- HiSat2 and Cufflinks
samtools cufflinks alignment rna-seq written 13 months ago by Lindsay44 • 0 • updated 13 months ago by Devon Ryan • 1.6k
4
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1
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283
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5 follow
1
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Filter Bowtie 2 alignement
samtools bowtie alignment written 13 months ago by Mic • 70 • updated 13 months ago by Devon Ryan • 1.6k
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1
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481
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1
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Visualizing mpileup data
bam samtools galaxy snp written 14 months ago by rquigl01 • 10 • updated 14 months ago by Jennifer Hillman Jackson ♦ 22k
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1
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614
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1
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how to extract mapped reads from output of BWA-MEM to a separate file?
samtools galaxy bwa-mem bwa mapping written 14 months ago by jerrry113 • 0 • updated 14 months ago by y.hoogstrate • 440
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1
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728
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1
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Normalization when convert bam to wig
bam samtools galaxy rna-seq written 14 months ago by rongruo1988 • 0 • updated 14 months ago by Jennifer Hillman Jackson ♦ 22k
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