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2
votes
5
replies
800
views
how to compare mapping of WES samples to human pangenome?
WES pangenome vg
8 months ago by bitpir ▴ 240
3
votes
5
replies
994
views
query UCSC db for CDS coordinates (Gencode)
CDS mysql UCSC bed
updated 13 months ago by 141k • written 13 months ago by ▴ 240
0
votes
1
reply
592
views
PF_INDEL_RATE calculation and definition
picard AlignmentSummaryMetrics picardmetrics
15 months ago by bitpir ▴ 240
0
votes
0
replies
343
views
QUAL differences for different caller
score vardict quality vcf freebayes calling variant
17 months ago by bitpir ▴ 240
0
votes
1
reply
656
views
variant analysis using Freebayes
calling freebayes false variant positives
updated 19 months ago by ▴ 230 • written 19 months ago by ▴ 240
0
votes
0
replies
323
views
understanding UMAP mappability bed file
UMAP mappability
2.1 years ago by bitpir ▴ 240
0
votes
2
replies
542
views
getting fastq ID with SNPs
SNP genome browser fastq
3.2 years ago by bitpir ▴ 240
2
votes
1
reply
1.1k
views
hsmetrics on_target_bases and on_baits_bases calculation
hsmetrics hybridization selection
updated 3.7 years ago by ▴ 40 • written 3.7 years ago by ▴ 240
0
votes
1
reply
2.5k
views
understanding pysam.AlignmentFile output
pysam sam bam
updated 4.3 years ago by ▴ 330 • written 4.3 years ago by ▴ 240
0
votes
2
replies
893
views
relationship between relative abundance and relative activity
meta-transcriptomics RNA-seq
updated 5.2 years ago by 20 • written 5.4 years ago by ▴ 240
0
votes
0
replies
1.0k
views
help with interpreting metagenomic metatranscriptomic data
meta-transcriptomic meta-genomic
5.3 years ago by bitpir ▴ 240
0
votes
0
replies
1.2k
views
measure relative abundance from rna-seq
RNA-Seq meta-transcriptomics
5.5 years ago by bitpir ▴ 240
1
vote
0
replies
1.6k
views
how to speed up cdhit clustering?
cdhit protein clustering nucleotide clustering
5.5 years ago by bitpir ▴ 240
1
vote
3
replies
2.0k
views
how to concatenate contigs from repseq?
refseq concatenate ncbi
updated 5.6 years ago by 35k • written 5.6 years ago by ▴ 240
0
votes
1
reply
798
views
tools/resources on mixed-integer programming
probability mixed-integer programming
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 240
0
votes
1
reply
931
views
taxa identification using signature vs alignment to refseq
alignment signatures refseq metagenomics
5.8 years ago by bitpir ▴ 240
1
vote
1
reply
1.6k
views
finding secondary taxid using ete3 ncbiTaxa
ete3 python ncbiTaxa taxonomyid
5.8 years ago by bitpir ▴ 240
1
vote
1
reply
3.3k
views
difference between mapq=0 and samtools flag 0x900
samtools mapq
updated 5.8 years ago by 104k • written 5.8 years ago by ▴ 240
0
votes
6
replies
1.3k
views
getting a combination of all predicted genes
bedtools gff
updated 5.9 years ago by 35k • written 5.9 years ago by ▴ 240
2
votes
5
replies
2.3k
views
getting feature annotations for all NCBI Refseq sequences
ncbi refseq annotation CDS
updated 6.0 years ago by 141k • written 6.0 years ago by ▴ 240
2
votes
4
replies
3.7k
views
IGV tracks gene annotation
IGV gene GFF
updated 6.0 years ago by 35k • written 6.0 years ago by ▴ 240
0
votes
0
replies
1.3k
views
complete and partial ORF identification
ORF gene prediciton Glimmer Genemark
6.0 years ago by bitpir ▴ 240
0
votes
4
replies
2.0k
views
Glimmer output file
ORF prediction Glimmer3
6.0 years ago by bitpir ▴ 240
4
votes
5
replies
2.6k
views
best way to do joint genotyping
gatk joint-genotyping vcf
updated 6.1 years ago by 20 • written 6.2 years ago by ▴ 240
3
votes
2
replies
1.4k
views
how does Agilent/xGen design hybridization probes?
exome sequencing custom probes
updated 6.2 years ago by ★ 1.7k • written 6.2 years ago by ▴ 240
3
votes
12
replies
4.3k
views
do blast search using gi numbers
blast
6.7 years ago by bitpir ▴ 240
4
votes
3
replies
7.8k
views
ncbi error C++ exception
blast ncbi
6.7 years ago by bitpir ▴ 240
0
votes
0
replies
2.1k
views
finding NCBI protein ID and associated COG ID
blastx nr database COG
6.8 years ago by bitpir ▴ 240
4
votes
3
replies
1.6k
views
customize reference genome
DNA-seq
updated 6.8 years ago by 47k • written 6.8 years ago by ▴ 240
0
votes
0
replies
969
views
software recommendations for identifying self from non-self dna sequences
forensics dna sequencing
6.8 years ago by bitpir ▴ 240
2
votes
1
reply
1.3k
views
CNVkit plotting tumor + healthy individuals
CNVkit software
updated 7.2 years ago by ★ 2.8k • written 8.0 years ago by ▴ 240
1
vote
4
replies
2.6k
views
Question about GATK hardfiltering conditions
gatk hardfiltering
updated 7.2 years ago by 20k • written 7.2 years ago by ▴ 240
0
votes
3
replies
1.7k
views
Total SNP calculation using command line vs picardtools
picardtools SNP
updated 7.6 years ago by 13k • written 7.6 years ago by ▴ 240
6
votes
17
replies
4.1k
views
fold enrichment calculation for exome sequencing
exome fold enrichment
7.7 years ago by bitpir ▴ 240
1
vote
2
replies
10k
views
samtools counting unique mapped reads
samtools read counts
updated 2.2 years ago by • 0 • written 7.8 years ago by ▴ 240
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