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4
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Forum: An entertaining read about BWA, Picard, GATK
galaxy software error forum bwa bam samtools written 3 months ago by apozhitkov • 40 • updated 3 days ago by linying9114 • 0
1
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0
answers
30
views
0
answers
Sample name on BedCov results
samtools bedcov written 14 days ago by shirley • 10
2
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2
answers
44
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5 follow
2
answers
Problem merging five 13.9 GB .BAM files
bam samtools written 17 days ago by rickwhite23 • 10
0
votes
1
answer
66
views
1
answer
How to generate pileup file
chip-seq samtools pileup usegalaxy.org usage written 5 weeks ago by dikshagarg0409 • 0 • updated 5 weeks ago by Jennifer Hillman Jackson ♦ 22k
4
votes
1
answer
142
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6 follow
1
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sam to bam - Galaxy version 17.01
galaxy samtools local job-error written 9 weeks ago by bryan.hepworth • 30 • updated 8 weeks ago by Jennifer Hillman Jackson ♦ 22k
1
vote
1
answer
113
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1
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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 3 months ago by msprindzhuk • 40 • updated 3 months ago by Jennifer Hillman Jackson ♦ 22k
0
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1
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119
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1
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Sam To Bam tool hangs in Cloning stage, though other tools, including Pilon, could be installed
samtools sam2bam written 3 months ago by msprindzhuk • 40 • updated 3 months ago by Jennifer Hillman Jackson ♦ 22k
0
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2
answers
143
views
2
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Removing sequence duplicates
samtools bowtie tophat written 3 months ago by msumaira36 • 0
0
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1
answer
288
views
1
answer
Interpreting Stats output of SAM tools
chip-seq samtools bam written 4 months ago by hpremathilake • 20 • updated 4 months ago by Jennifer Hillman Jackson ♦ 22k
0
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1
answer
164
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1
answer
MAF to VCF showing Indels and snps
samtools alignment written 4 months ago by kmurph55 • 0 • updated 4 months ago by Jennifer Hillman Jackson ♦ 22k
2
votes
3
answers
179
views
5 follow
3
answers
Flow issues? (no temp SAM/BAM to start run?)
bam samtools usegalaxy.org workflow written 6 months ago by dragon28 • 30
0
votes
1
answer
166
views
1
answer
Can't do sam to bam conversion
samtools bowtie snp written 6 months ago by tanvee • 0 • updated 6 months ago by Jennifer Hillman Jackson ♦ 22k
2
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3
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240
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3
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Mapping using multiple reference sequences
reference mapping samtools bwa bam written 7 months ago by Juan Ledesma • 0
0
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1
answer
395
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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 7 months ago by pilargomez91 • 0 • updated 7 months ago by Jennifer Hillman Jackson ♦ 22k
0
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1
answer
193
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1
answer
Upload Jatropha Reference genome for Bowtie2
samtools galaxy bowtie alignment bwa written 7 months ago by anoopanandmalik • 0 • updated 7 months ago by Jennifer Hillman Jackson ♦ 22k
2
votes
2
answers
576
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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 8 months ago by deane • 20 • updated 8 months ago by Jennifer Hillman Jackson ♦ 22k
2
votes
5
answers
723
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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 21 months ago by jmnm2201 • 0 • updated 8 months ago by Jennifer Hillman Jackson ♦ 22k
3
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2
answers
466
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2
answers
HISAT2 "OSError: [Errno 2] No such file or directory" (Samtools install problem on a local Galaxy)
samtools local error admin hisat written 8 months ago by djevo1 • 40 • updated 8 months ago by Jennifer Hillman Jackson ♦ 22k
0
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1
answer
290
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1
answer
'BEDcov' and 'compute depth and breadth'
bam samtools coverage bed bedtools written 8 months ago by c.zijlstra • 0 • updated 8 months ago by Jennifer Hillman Jackson ♦ 22k
1
vote
1
answer
290
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1
answer
Error: "Samtools not found" on a local Galaxy when running other jobs
samtools local galaxy hisat rna-seq written 8 months ago by djevo1 • 40 • updated 8 months ago by Jennifer Hillman Jackson ♦ 22k
0
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1
answer
214
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1
answer
Low data conversion rate for BAM-to-SAM. Fix Database, Datatype, Sorting
bam samtools database datatype fastq written 8 months ago by cwalker912 • 0 • updated 8 months ago by Jennifer Hillman Jackson ♦ 22k
1
vote
6
answers
470
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6
answers
Bam File error uploading
samtools error admin path upload written 10 months ago by shambyross • 10 • updated 9 months ago by y.hoogstrate • 440
2
votes
2
answers
299
views
2
answers
No space left on device error (filezilla and processing jobs)
chip-seq samtools galaxy software error bwa written 9 months ago by k.vanduijvenboden • 10 • updated 9 months ago by a.turtoi • 50
1
vote
1
answer
350
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1
answer
mpileup error: reference sequence is not being fetched correctly?
samtools mpileup reference genome dbkey written 9 months ago by mkim3 • 10 • updated 9 months ago by Jennifer Hillman Jackson ♦ 22k
1
vote
1
answer
257
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1
answer
How to access datacollection metadata (input names of elements)
samtools tool development metadata data collection written 9 months ago by fiebig • 30
0
votes
1
answer
205
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1
answer
Missing genome for SAM-to-BAM conversion
samtools database metadata tool input written 9 months ago by nicholas.anthony • 0 • updated 9 months ago by Jennifer Hillman Jackson ♦ 22k
0
votes
0
answers
258
views
0
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Cuffdiff Error- empty output files URGENT
samtools cufflinks rna-seq written 10 months ago by Lindsay44 • 0
0
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0
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285
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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 11 months ago by Jennifer Hillman Jackson ♦ 22k
1
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1
answer
998
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1
answer
RNA-seq analysis- HiSat2 and Cufflinks
samtools cufflinks alignment rna-seq written 12 months ago by Lindsay44 • 0 • updated 11 months ago by Devon Ryan • 1.5k
4
votes
1
answer
252
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5 follow
1
answer
Filter Bowtie 2 alignement
samtools bowtie alignment written 11 months ago by Mic • 70 • updated 11 months ago by Devon Ryan • 1.5k
0
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1
answer
407
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1
answer
Visualizing mpileup data
bam samtools galaxy snp written 12 months ago by rquigl01 • 10 • updated 12 months ago by Jennifer Hillman Jackson ♦ 22k
0
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1
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548
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1
answer
how to extract mapped reads from output of BWA-MEM to a separate file?
samtools galaxy bwa-mem bwa mapping written 12 months ago by jerrry113 • 0 • updated 12 months ago by y.hoogstrate • 440
0
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1
answer
608
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1
answer
Normalization when convert bam to wig
bam samtools galaxy rna-seq written 12 months ago by rongruo1988 • 0 • updated 12 months ago by Jennifer Hillman Jackson ♦ 22k
0
votes
1
answer
332
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1
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Need help with mpileup tool on Galaxy
samtools mpileup galaxy written 12 months ago by errityf • 0 • updated 12 months ago by Jennifer Hillman Jackson ♦ 22k
0
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0
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216
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0
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Mate_Not_Found after FixMate and filter
bam samtools medip-seq written 13 months ago by nhs • 0 • updated 13 months ago by Jennifer Hillman Jackson ♦ 22k
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