User: bruce.moran

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bruce.moran240
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Posts by bruce.moran

<prev • 72 results • page 1 of 8 • next >
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Comment: C: Pipe BBMap reformat output into SAMtools
... My RTFM is strong (also helps that there is a good FM) ...
written 8 days ago by bruce.moran240
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Comment: C: Pipe BBMap reformat output into SAMtools
... Thought about that also, but yes, using kmers. ...
written 8 days ago by bruce.moran240
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Comment: C: Pipe BBMap reformat output into SAMtools
... Cool, I had to use addslash and underscore hence the reformat.sh, but good to know. ...
written 8 days ago by bruce.moran240
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Answer: A: Pipe BBMap reformat output into SAMtools
... To answer my own Q: bbduk.sh in1=6484_snippet_1.fastq \ in2=6484_snippet_2.fastq \ trimq=30 out=stdout.fq \ | reformat.sh in=stdin.fq \ out=stdout.bam \ | samtools view -hb - | samtools reheader 6484_snippet_header.sam - > 6484_snippet.r ...
written 10 days ago by bruce.moran240
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Comment: C: Pipe BBMap reformat output into SAMtools
... OK, I had read that, just tried a few things and it seems you have to stream through `samtools view`: reformat.sh in=6484_snippet_1.fastq out=stdout.bam | samtools reheader 6484_snippet_header.sam - > 6484_snippet.rh.bam returns `[W::hts_close] EOF marker is absent. The input is probably tr ...
written 10 days ago by bruce.moran240
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Pipe BBMap reformat output into SAMtools
... Hi all, I am wondering if I can pipe output from `reformat.sh` in BBMap into SAMtools `view`. My goal is to take a set of fastq and return an unaligned BAM headed with sequence dictionary (this is for use in GATK4). Using some [GATK test data][1] this part works (of course!): bbduk.sh in1=6484 ...
bbmap samtools pipe written 10 days ago by bruce.moran240
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Answer: A: In FACETS, what does the mafR value represent?
... Probably a bit old but I am working through this method, so: ?procSample ... 'mafR’ the log-odds-ratio summary for the segment This represents the ratio of counts of heterozygous sites in the tumour/normal pair (log-ratio is the ratio of total counts in tumour/normal pair). The idea be ...
written 11 days ago by bruce.moran240
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Comment: C: Are there NGS-based CNV callers that utilise allele frequency?
... +1, was also looking for a read depth and BAF method, and FACETS is just that. Senior author was involved in developing circular binary segmentation. ...
written 11 days ago by bruce.moran240
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Comment: C: BWA option about the insert size
... Without reference, and much faster, is BBMerge (what a surprise that it's part of BBMap!), with a little command line addition to catch output in a text file and allow it to be output to screen also: bbmerge.sh in1=r1.fq in2=r2.fq out=merged.fq 2>&1 | tee insert.txt ...
written 24 days ago by bruce.moran240
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Comment: C: Subtracting contamination from RNASeq data
... I see where you are coming from, and I follow the logic. What if you estimate the contamination proportion using genes only expressed in MEFs, then remove per library/sample avoiding the bias? No idea how to incorporate that change in variance. BTW may be helpful to give a blow-by-blow account of wh ...
written 26 days ago by bruce.moran240

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