User: taffners

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taffners0
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Posts by taffners

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Masking phages, mobile elements, and transposons before calling SNP's
... I need to mask phages, mobile elements, and transposons before calling SNP's in my bacterial genome. How should I go about doing this? I have found the coordinates to mask by annotating my reference genome with [RAST][1]. I was planning on trying to mask my genome before mapping but I have found ...
bacteria snp written 4 weeks ago by taffners0 • updated 4 weeks ago by genomax37k
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How to run Breseq. FASTQ sequence record does not begin with @NAME line error.
... I running breseq. I'm getting the error: FASTQ sequence record does not begin with @NAME line. I'm exactly sure what this means. I can't find anything about @NAME and FASTQ files. I was thinking it meant add a line to the top of the file to identify the fastq file. So I added @NAME 8_cre_urmc ...
fastq breseq written 10 weeks ago by taffners0 • updated 10 weeks ago by h.mon9.2k
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Bowtie2 Alignment for breadth of coverage using -U and --no-unal taking a long time
... I'm have been trying to follow the post below to calculate breadth of coverage. However, the alignment step appears to be not working. http://www.metagenomics.wiki/tools/samtools/breadth-of-coverage I'm trying to run the alignment with the following command but it has been running now for 1.5 h ...
bowtie2 written 3 months ago by taffners0

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