User: ambi1999

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ambi199930
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Posts by ambi1999

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Comment: A: Error running BWA-MEM or Bowtie2 in usegalaxy
... Thx Jen. I had guessed something like that because it seemed more like a memory error and coming up for lot of tools. Cheers, Ambi. ...
written 4 months ago by ambi199930
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Error running BWA-MEM or Bowtie2 in usegalaxy
... Hi, I am getting following errors while trying to run BWA-MEM or bowtie2 in usegalaxy. The input files are two fastq files and datatype is fastqsanger. BWA-MEM An error occurred setting the metadata for this dataset Set it manually or retry auto-detection sort: invalid option -- 'O' [main] unrec ...
bowtie2 usegalaxy.org job bwa-mem error written 4 months ago by ambi199930
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New Fasta Sequence From Variant Calls File
... Hi, Is there a way in Galaxy to create a new FASTA reference sequence from a reference sequence and vcf file? Sometime similar to GATK FastaAlternateReferenceMaker. Cheers, Ambi. ...
vcf fasta written 18 months ago by ambi199930
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empty QUAL filed in Naive Variant caller vcf output
... Hi, The QUAL field in vcf output of Naive Variant Caller is empty for all the variants. Any reason? Attached is screenshot of the vcf. I will email my galaxy history link to galaxy-bugs@lists.galaxyproject.org, and include a link to this post so you can associate the two. Note: I do get QUAL val ...
variant caller vcf qual naive variant caller written 19 months ago by ambi199930
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Subtract one VCF file from another VCF file
... Hi, Is there a way in Galaxy to subtract one VCF file from another to get a VCF file containing just the SNPs unique to one of the samples? I have tried Subtract Whole Dataset under 'Join, Subtract and Group' but it does not seem to work give me the correct answer. ps: I know subtract in bedtool ...
vcf snp written 19 months ago by ambi199930 • updated 19 months ago by Jennifer Hillman Jackson25k

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