Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

User: QVINTVS_FABIVS_MAXIMVS

gravatar for QVINTVS_FABIVS_MAXIMVS
Reputation:
2,340
Status:
Trusted
Location:
USA SoCal
Last seen:
10 hours ago
Joined:
5 years, 11 months ago
Email:
d********@gmail.com

There's more than one way to hunt a CNV

Posts by QVINTVS_FABIVS_MAXIMVS

<prev • 240 results • page 1 of 24 • next >
1
vote
1
answer
69
views
1
answer
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 12 days ago by QVINTVS_FABIVS_MAXIMVS • 2.3k • updated 12 days ago by igor ♦ 9.2k
0
votes
1
answer
95
views
1
answers
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 4 weeks ago by QVINTVS_FABIVS_MAXIMVS • 2.3k
0
votes
2
answers
101
views
2
answers
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 4 weeks ago by QVINTVS_FABIVS_MAXIMVS • 2.3k
0
votes
1
answer
95
views
1
answer
Missing MQ tag from bwa mem alignments
... I am using BWA MEM 0.7.17 for all my paired-end alignments. Can someone clue me in on why some alignments have a `MQ` tag and others do not? The commands are identical in some cases. Does BQSR apply this tag, there could be a difference in the options at this step perhaps? And I think some align ...
wgs mem alignment bwa written 4 weeks ago by QVINTVS_FABIVS_MAXIMVS • 2.3k • updated 4 weeks ago by benformatics • 1.3k
0
votes
0
answers
73
views
0
answers
BQSR BD/BI Tags into integer values?
... I want to convert the values in the BI and BD tags into integer values. However, I cannot find any documentation online that has the conversion table. If someone knows where I can find this, please link me to it! ...
gatk bqsr written 4 weeks ago by QVINTVS_FABIVS_MAXIMVS • 2.3k
0
votes
3
answers
2.7k
views
3
answers
Answer: A: Is GRCh37 and hg19 are the same?
... GRCh37d5 is different since there is a decoy sequence that may not be present in some hg19 builds. Also if memory serves me GRCh37 with or without decoy hard masks the pseudoautosomal regions on chrY, therefore you treat the pseudoautosomal region on chrX as diploid in males. I do not think some of ...
written 4 weeks ago by QVINTVS_FABIVS_MAXIMVS • 2.3k
0
votes
0
answers
121
views
0
answers
BED to HDF5 in Python. Simple Script?
... I'm looking for some simple boilerplate script that efficiently converts a BED file (only Chrom Start End) to HDF5 in python. All the examples I see online are convoluted and bloated with functions that I do not need (HI-C/GTF). I do not need a CLI script, I would like to implement a BED -> H ...
python hdf5 bed written 3 months ago by QVINTVS_FABIVS_MAXIMVS • 2.3k
4
votes
1
answer
204
views
1
answer
Alternatives to CNVnator?
... I think I have put over 36 man hours in trying to get CNVnator to install. I have tried nearly every avenue, conda, environments, etc... and still cannot get it to install. I am at my wits end, what are comparable CNV calling algorithms for whole genomes that use read depth. Basically I'm looking ...
copy number variation cnv written 3 months ago by QVINTVS_FABIVS_MAXIMVS • 2.3k • updated 3 months ago by jared.andrews07 • 4.3k
8
votes
3
answers
247
views
3
answers
Samtools view -f "OR" operator possible?
... Quick question: Is it possible to do a `samtools view -f XXX` using a `OR` operator? Say if I wanted to get all reads that were unmapped (`4`) or supplementary alignments (`2048`). Is this possible? Because doing a `2052` is an "AND" (reads are unmapped and supplementary alignments which is imp ...
samtools written 6 months ago by QVINTVS_FABIVS_MAXIMVS • 2.3k • updated 6 months ago by dariober ♦ 10k
0
votes
1
answer
546
views
1
answers
Comment: C: BWA MEM Definition of a Primary Alignment
... Thanks for not answering my question. For chimeric reads (i.e for this example true split-reads that for SV informative) the difference between secondary and supplementary is semantic, a secondary alignment would map to another position but be clipped in a manner that is supporting a breakpoint. Som ...
written 7 months ago by QVINTVS_FABIVS_MAXIMVS • 2.3k

Latest awards to QVINTVS_FABIVS_MAXIMVS

Popular Question 12 days ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 3 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Student 3 months ago, asked a question with at least 3 up-votes. For LAST Aligner: last-train output
Great Question 3 months ago, created a question with more than 5,000 views. For Split Read in Samtools
Popular Question 3 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Start position of structural variants in 1000 Genomes
Popular Question 6 months ago, created a question with more than 1,000 views. For Are XA: tagged reads == SA: tagged BWAMEM aligned reads?
Popular Question 6 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 10 months ago, created a question with more than 1,000 views. For Position of N nucleotides in reference genome
Popular Question 10 months ago, created a question with more than 1,000 views. For Are XA: tagged reads == SA: tagged BWAMEM aligned reads?
Student 10 months ago, asked a question with at least 3 up-votes. For Picard CollectWgsMetrics for each chromosome? Standard deviation of coverage per chromosome
Popular Question 10 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 12 months ago, created a question with more than 1,000 views. For Combining ENCODE narrowPeak BED files across replicates
Popular Question 12 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 12 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Start position of structural variants in 1000 Genomes
Popular Question 19 months ago, created a question with more than 1,000 views. For Combining ENCODE narrowPeak BED files across replicates
Popular Question 19 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Prophet 19 months ago, created a post with more than 20 followers. For Difference between Hard Clip and Soft Clip in Samtools CIGAR string
Great Question 19 months ago, created a question with more than 5,000 views. For Difference between Hard Clip and Soft Clip in Samtools CIGAR string
Great Question 19 months ago, created a question with more than 5,000 views. For cannot import pysam. Module has no attribute error
Appreciated 19 months ago, created a post with more than 5 votes. For A: 1000Genome SV integrated map's power for SV filter
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1073 users visited in the last hour