User: mark.rose

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mark.rose10
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New User
Location:
United States
Last seen:
4 hours ago
Joined:
3 years, 8 months ago
Email:
m********@syngenta.com

Posts by mark.rose

<prev • 53 results • page 1 of 6 • next >
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IGV SNP glyph question
... Hi All I'm visualizing an alignment of Illumina paired end data in IGV. Some of the SNPs observed are rendered as glyphs consisting of a solid bar where as others appear as a bar with a gap in the middle. Looking at the alignment it appears that the gapped bar occurs where read1 and read2 do not ...
snp igv written 5 hours ago by mark.rose10
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Comment: C: bbmap paired-end alignment problem
... Thanks for the tip ...
written 7 weeks ago by mark.rose10
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Comment: C: bbmap paired-end alignment problem
... I checked the FLAG and you are indeed correct, one is read1 and the other read2 despite their QNAMEs. So I guess all is fine, if unexpected, in regard to the representation of paired-ends. Thanks for your help. As for samtools, I'm using version 0.1.19-44428cd. ...
written 7 weeks ago by mark.rose10
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Comment: C: bbmap paired-end alignment problem
... [rosema1@demeter trunk]$ samtools view -f 0x0040 out.sam | wc -l [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "out.sam". 0 [rosema1@de ...
written 7 weeks ago by mark.rose10 • updated 7 weeks ago by genomax46k
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bbmap paired-end alignment problem
... Hi All I'm having a problem with aligning Illumina PE reads with BBMap version 35.92. Execution of bbmap.sh overwrite=t ref=Z.fasta in=R1_001_val_1.100.fq in2=R2_001_val_2.100.fq minid=0.25 mappedonly=true out=out.sam outu=unaligned_reads.fa maxindel=100000 yields out.sam which contains on ...
paired-end bbmap align written 7 weeks ago by mark.rose10
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Comment: C: freebayes haplotype calling (phased variants)
... As I work for a private company, I cannot share my code with you. Sorry. If you can code or have access to someone who can, I could describe it to you a bit more and you could attempt to create your own version. ...
written 9 weeks ago by mark.rose10
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Comment: C: freebayes haplotype calling (phased variants)
... As I recall I was able to get some haplotype calling but it was erratic and failed to accurately represent simulated data. Your objective seems much like mine was. What I wound up doing was to write a pipeline which would analyze read pairs from amplicons individually and then identify sets of var ...
written 10 weeks ago by mark.rose10
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Comment: C: jellyfish configure script problem
... Yes, that did the trick. Note that I downloaded jellyfish from github where version 1.1.10 was the latest version 1 available. To get 1.1.11 I had to go to the cbcb site. Much thanks ...
written 10 weeks ago by mark.rose10
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jellyfish configure script problem
... Hi All Trying to install an old version of jellyfish (v1.1.10) as is required by Kraken but I am geting the following error. Can you help? Thanks Mark $ autoconf $ ./configure --prefix=/SD5/people/rosema1/BioInfo/bin/jellyfish-1.1.10 configure: error: cannot find install-sh or ...
jellyfish kraken configure written 11 weeks ago by mark.rose10
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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 5 months ago by mark.rose10

Latest awards to mark.rose

Popular Question 9 months ago, created a question with more than 1,000 views. For freebayes haplotype calling (phased variants)
Popular Question 9 months ago, created a question with more than 1,000 views. For discordant alignments when bowtie2 set to --no-discordant
Popular Question 3.2 years ago, created a question with more than 1,000 views. For unexpected bowtie2 unpaired alignment behavior

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