User: mark.rose

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mark.rose10
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United States
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1 week, 4 days ago
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3 years, 5 months ago
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m********@syngenta.com

Posts by mark.rose

<prev • 44 results • page 1 of 5 • next >
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Comment: C: IGV tracks fail to render even after zooming
... I am launching it on a windows machine with a igv.bat file. When I do so a terminal window as well as the viewer appears. There is no error message in the terminal just the usual startup info ![https://ibb.co/gij7nb][1] Also I tried upgrading to version 2.4.4. No difference. I then tried droppi ...
written 9 weeks ago by mark.rose10
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Comment: C: IGV tracks fail to render even after zooming
... Well I looked more online and found some people using tabix for indexing bed files for IGV and so that is what I did (after commenting the header) sort -k1,1 -k2,2n test.strand_bias.bedgraph | bgzip > test.strand_bias.bedgraph.gz; tabix -s 1 -b 2 -e 3 test.strand_bias.bedgraph.gz I then substi ...
written 9 weeks ago by mark.rose10
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Comment: C: IGV tracks fail to render even after zooming
... I presume you mean with tabix. No, but I have never done that in the past and never, in the many times I've done this, had any issue. Is there a reason why indexing would be needed in some cases but not others? This is a smaller reference than I have used in the past. ...
written 9 weeks ago by mark.rose10
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IGV tracks fail to render even after zooming
... Hi All I have a tool that performs alignment against a reference sequence and then creates an IGV session file based on that alignment and other features of the reference sequence. genome="dataset_18581.dat" locus="dataset_18581.dat" version="3" ...
track igv written 9 weeks ago by mark.rose10 • updated 9 weeks ago by Jim Robinson220
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Comment: C: INDEL left alignment in bam and vcf
... Hey Brian Thanks for the suggestion. Worked like a charm. Will look more into the bbmap package. Mark ...
written 11 months ago by mark.rose10
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INDEL left alignment in bam and vcf
... Hello I am performing alignments of amplicons against a reference. Many of these amplicons have sizeable deletions. When aligning reads with such deletions, some aligners (bowtie2, bwa) soft clip the reads or fail to align them. Others, like blasr, produce an alignment which successfully spans the ...
indel aligner bowtie bwa blasr written 11 months ago by mark.rose10 • updated 11 months ago by Brian Bushnell15k
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Comment: C: BG7 usage for bacterial genome annotation
... Yes, I've seen these papers. The first one is more practical in that it purports to describe how to execute BG7. That's where I run into trouble. In what I have downloaded from github, there is no executable called "BG7", only "bg7", which is a shell script and does take any of the commands (crea ...
written 14 months ago by mark.rose10
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Comment: C: varscan misses alternate variant alleles
... Should have included the lofreq vcf #CHROM POS ID REF ALT QUAL FILTER INFO ZmpylD 167 . G C 1261 PASS DP=193;AF=0.305699;SB=0;DP4=134,0,59,0 ZmpylD 168 . A T 1315 PASS DP=193;AF=0.305699;SB=0;DP4=134,0,59,0 ...
written 14 months ago by mark.rose10
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Comment: C: varscan misses alternate variant alleles
... Yes, preprocessing the bam file with lofreq indelqual did the trick. Thanks a lot. Still toying with the idea of calling variants on an individual read level though, then setting thresholds on frequency to eliminate sequencing error. The main advantage of doing this, now that the multi-allelic va ...
written 14 months ago by mark.rose10
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Comment: C: varscan misses alternate variant alleles
... Tried this as you suggested $ ~/BioInfo/bin/lofreq_star-2.1.2/bin/lofreq call --no-baq --call-indels -f my_ref.fa my.bam ##fileformat=VCFv4.0 ##fileDate=20161122 ##source=/SD5/people/rosema1/BioInfo/bin/lofreq_star-2.1.2/bin/lofreq call --no-baq --call-indels -f my_ref.fa my.bam ...
written 14 months ago by mark.rose10

Latest awards to mark.rose

Popular Question 6 months ago, created a question with more than 1,000 views. For freebayes haplotype calling (phased variants)
Popular Question 6 months ago, created a question with more than 1,000 views. For discordant alignments when bowtie2 set to --no-discordant
Popular Question 2.9 years ago, created a question with more than 1,000 views. For unexpected bowtie2 unpaired alignment behavior

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