User: QVINTVS_FABIVS_MAXIMVS

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There's more than one way to hunt a CNV

Posts by QVINTVS_FABIVS_MAXIMVS

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Comment: C: Determine Reading Frame from Exon Genomic Positions (rMATS)
... Do you have an example because I tried using blastx on my skipped exon sequence and it didn't return anything. The exon is annotated in a GTF in RefSeq which is odd. ...
written 8 days ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Determine Reading Frame from Exon Genomic Positions (rMATS)
... I realize that given an exon start and stop position, the reading frame CANNOT be inferred by starting at the start position making codons. So my question is how to computationally determine the reading frame of an exon given the START and END positions? Specifically I am using the output from rM ...
rmats genome rna-seq written 8 days ago by QVINTVS_FABIVS_MAXIMVS2.4k • updated 8 days ago by swbarnes28.9k
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Comment: C: Ensembl FTP Mirror in USA? Slow Downloads
... Thanks I submitted a ticket. Hopefully they will clear it up. ...
written 5 weeks ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Comment: C: Ensembl FTP Mirror in USA? Slow Downloads
... ``` $ curl -O ftp://ftp.ensembl.org/pub/release-101/variation/indexed_vep_cache/homo_sapiens_merged_vep_101_GRCh38.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 16.4G 0 13.8M ...
written 5 weeks ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Ensembl FTP Mirror in USA? Slow Downloads
... Hello I work on a fairly good cluster at an R1 university in the USA. I am downloading the VEP 101 indexed cache files and it's slow as Christmas. I mean AOL speeds slow. If I download a similar size file from AWS or NCBI it's extremely fast. Is there a mirror for the USA containing the VEP cache ...
ensembl vep written 5 weeks ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Comment: C: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotatio
... Hey this is a great example. I mentor undergrads in my lab and they could use this video from time to time! Thanks for sharing ...
written 11 weeks ago by QVINTVS_FABIVS_MAXIMVS2.4k
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MarkDups takes much longer than expected???
... In the past, my 40x WGS BAMs take about 2-6 hours to run sambamba markdups with 12-24 threads. I have received a batch of BAMs that are taking over 7 days to run. The file size is the same, and so is the sequencing center. Any ideas what could cause this step to take much longer than expected? ...
markdup sambamba written 7 months ago by QVINTVS_FABIVS_MAXIMVS2.4k • updated 6 months ago by Biostar ♦♦ 20
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Mouse Strains in mm10/GRCm38 dbSNP 142?
... I am using the pre-built HiSat2 index for mm10 with the snps. Looking at the script the devs provide, I can see they are using SNPs from UCSC golden path. https://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/snp142Common.txt.gz However, I would like to know which strains are included for this r ...
mm10 hisat2 dbsnp mouse written 9 months ago by QVINTVS_FABIVS_MAXIMVS2.4k • updated 9 months ago by igor11k
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Comment: C: Missing MQ tag from bwa mem alignments
... I was referring to SAM/BAM file MQ tag. Unfortunately sometimes I have to use legacy code. ...
written 10 months ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Answer: A: lumpy for cnv detection
... You should merge the SVs and genotype them. Hopefully your plant is diploid since svtyper is for diploid organisms. Perhaps, it can handle higher ploidies. I would follow the methods outlined in this paper https://www.nature.com/articles/s41467-018-06159-4 The developers of lumpy/svtyper contribu ...
written 10 months ago by QVINTVS_FABIVS_MAXIMVS2.4k

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