User: William

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William4.7k
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Posts by William

<prev • 323 results • page 1 of 33 • next >
2
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Answer: A: Plotting marker location co-linearity between multiple physical and genetic maps
... RIdeogram seems to be able to do what I am looking for: https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html ...
written 5 months ago by William4.7k
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Comment: C: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
... There is no information under Check8. I'll wait for the next release for the extra logging. I also ran the gff3 file fixed by AGAT trough our internal gff3 validator, it complains about duplicate UTR ids. After removing the UTR records (which are implied by the exon and CDS differences), the valid ...
written 5 months ago by William4.7k
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Comment: C: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
... `agat_sp_gxf_to_gff3.pl` did fix the sorting issue, and also added explicit UTR records (which are already implied by the exon to CDS differences). This seems to have fixed the downstream issue also that depends on the correct sorting. Strange thing is that after running `agat_sp_gxf_to_gff3.pl` ...
written 5 months ago by William4.7k
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Plotting marker location co-linearity between multiple physical and genetic maps
... I am trying to plot the co-linearity of marker locations on multiple physical and genetic maps. I am not trying to improve the physical maps via the genetic maps, I just want to plot the co-linearity to see the discordance and the few discordances. I have a reference genome based on short reads, ...
plotting ideogram written 5 months ago by William4.7k
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Comment: C: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
... Thank you, I'll give both options in AGAT a try. ...
written 6 months ago by William4.7k
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Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
... Is it possible to sort a gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS). The order of the featuretypes is important when converting a gff file to a gtf file with gffread. If the mRNA record is before the gene record, then the gene_id and gene_name are not set in the l ...
gff3 written 6 months ago by William4.7k
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Comment: C: Custom TruSeq-equivalent WGS library preps, for high number of smal genomes
... Ok thank you. I'll move the post elsewhere. ...
written 6 months ago by William4.7k
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(Closed) Custom TruSeq-equivalent WGS library preps, for high number of smal genomes
... Does anyone have experience with custom "TruSeq-equivalent WGS library preps"? Normal TruSeq library prep costs around somewhere between $300 to $150 per sample. Some providers offer custom "TruSeq-equivalent WGS library preps" for 48 or 96 sample plates at a cost of around $60 per sample. Especi ...
ngs written 6 months ago by William4.7k
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How to remove duplicate reads / create consensus reads based on umi tags in 2nd fastq file?
... In a targeted sequencing dataset, I have for each sample a `r1.fastq.gz` file and a `umi.fastq.gz` file. How can I use the short umi tags that are in the `umi.fastq.gz` file, to remove duplicates or create a consensus sequence of the reads in the `r1.fastq.gz` file? Or do I need to go back to, o ...
umi written 9 months ago by William4.7k
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Comment: C: Difference between . and ./. for missing genotype in VCF
... The single record is from the output of a recent variant calling of a diploid organism with GATK4. GATK4 variant called multiple samples via GenotypeGVCFs (i.e. there was intermediate GVCF output that was later merged). ...
written 23 months ago by William4.7k

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Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Multi-Sample Vcf To Phylogenetic Tree.
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