User: Joe Fass

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Joe Fass180
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Posts by Joe Fass

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Has Anyone Successfully Used The Bioconductor Shortread Package To Read In Pacbi
... Ahem. From the help for readAligned(): [?] So, no PacBio BAM files in ShortRead. Leaving this up as a testament to not thoroughly reading the documentation. ...
written 7.7 years ago by Joe Fass180
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Has Anyone Successfully Used The Bioconductor Shortread Package To Read In Pacbio Read Alignments, In Sam/Bam Format?
... I've aligned PacBio subreads (fasta) to a reference using Heng Li's BWA (the long read aligner - BWA-SW, using the command 'bwa bwasw'), and I'm trying to read these in using > r = readAligned("test.bam", type="BAM") Now, I know there's a potential problem here, in that BWA-SW will produce mul ...
short R bioconductor bam written 7.7 years ago by Joe Fass180
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Answer: A: How To Do Multiple Whole Genomes Alignments?
... I've used Mauve (http://gel.ahabs.wisc.edu/mauve/) in the past. If you're aligning relatively complete assemblies, it might be what you're looking for. It also has a feature ("move contigs" or contig reordering) where it will rearrange contigs (from, say, a draft assembly) until they're in an order ...
written 8.0 years ago by Joe Fass180
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Answer: A: What'S Causing Ridiculous Md Tags In My Sam Files, After Aligning Paired Reads W
... Argh, argh, argh. Thank you so much swbarnes2! I was checking the wrong set of commands, and indeed, I'd aligned the forward reads for both the forward.sai and reverse.sai results, but not the sampe command. So sampe was reading the correct reverse reads from their fastq file, but was using the alig ...
written 8.4 years ago by Joe Fass180
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Comment: C: What'S Causing Ridiculous Md Tags In My Sam Files, After Aligning Paired Reads W
... Must be an "answer"-only feature ... or question ... ...
written 8.4 years ago by Joe Fass180
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Comment: C: What'S Causing Ridiculous Md Tags In My Sam Files, After Aligning Paired Reads W
... ohhhhh ... tabs? how about this? no? ...
written 8.4 years ago by Joe Fass180
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Comment: C: What'S Causing Ridiculous Md Tags In My Sam Files, After Aligning Paired Reads W
... how about this: [?][?]final attempt[?][?] ...
written 8.4 years ago by Joe Fass180
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Comment: C: What'S Causing Ridiculous Md Tags In My Sam Files, After Aligning Paired Reads W
... yah ... triple- and quadruple-checked those things. Also re-indexed reference with exact same version of BWA that I'm using for the aln and sampe steps. Baffling ... ...
written 8.4 years ago by Joe Fass180
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Comment: C: What'S Causing Ridiculous Md Tags In My Sam Files, After Aligning Paired Reads W
... nope ... [?]try again?[?] ...
written 8.4 years ago by Joe Fass180
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Comment: C: What'S Causing Ridiculous Md Tags In My Sam Files, After Aligning Paired Reads W
... Thanks Pierre -- how'd you make the text box ... like this?[?]example output[?] ...
written 8.4 years ago by Joe Fass180

Latest awards to Joe Fass

Teacher 7.7 years ago, created an answer with at least 3 up-votes. For A: Has Anyone Successfully Used The Bioconductor Shortread Package To Read In Pacbi
Student 8.4 years ago, asked a question with at least 3 up-votes. For What'S Causing Ridiculous Md Tags In My Sam Files, After Aligning Paired Reads With Bwa?
Appreciated 8.8 years ago, created a post with more than 5 votes. For Anyone Know A *General* Variant (Snp/Indel) Effect Predictor / Annotator?
Good Question 8.8 years ago, asked a question that was upvoted at least 5 times. For Anyone Know A *General* Variant (Snp/Indel) Effect Predictor / Annotator?
Popular Question 8.8 years ago, created a question with more than 1,000 views. For Anyone Know A *General* Variant (Snp/Indel) Effect Predictor / Annotator?
Student 8.8 years ago, asked a question with at least 3 up-votes. For Anyone Know A *General* Variant (Snp/Indel) Effect Predictor / Annotator?

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