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2
votes
5
replies
1.8k
views
how to compare mapping of WES samples to human pangenome?
WES pangenome vg
2.2 years ago by bitpir ▴ 250
3
votes
5
replies
2.0k
views
query UCSC db for CDS coordinates (Gencode)
CDS mysql UCSC bed
updated 2.6 years ago by 154k • written 2.6 years ago by ▴ 250
0
votes
1
reply
1.0k
views
PF_INDEL_RATE calculation and definition
picard AlignmentSummaryMetrics picardmetrics
2.8 years ago by bitpir ▴ 250
0
votes
0
replies
685
views
QUAL differences for different caller
score vardict quality vcf freebayes calling variant
3.0 years ago by bitpir ▴ 250
0
votes
1
reply
1.2k
views
variant analysis using Freebayes
calling freebayes false variant positives
updated 3.1 years ago by ▴ 250 • written 3.1 years ago by ▴ 250
0
votes
0
replies
644
views
understanding UMAP mappability bed file
UMAP mappability
3.6 years ago by bitpir ▴ 250
0
votes
2
replies
887
views
getting fastq ID with SNPs
SNP genome browser fastq
4.7 years ago by bitpir ▴ 250
2
votes
1
reply
1.5k
views
hsmetrics on_target_bases and on_baits_bases calculation
hsmetrics hybridization selection
updated 5.2 years ago by ▴ 40 • written 5.3 years ago by ▴ 250
0
votes
1
reply
3.0k
views
understanding pysam.AlignmentFile output
pysam sam bam
updated 5.8 years ago by ▴ 330 • written 5.8 years ago by ▴ 250
0
votes
2
replies
1.3k
views
relationship between relative abundance and relative activity
meta-transcriptomics RNA-seq
updated 6.8 years ago by 20 • written 6.9 years ago by ▴ 250
0
votes
0
replies
1.3k
views
help with interpreting metagenomic metatranscriptomic data
meta-transcriptomic meta-genomic
6.8 years ago by bitpir ▴ 250
0
votes
0
replies
1.4k
views
measure relative abundance from rna-seq
RNA-Seq meta-transcriptomics
7.0 years ago by bitpir ▴ 250
1
vote
0
replies
1.9k
views
how to speed up cdhit clustering?
cdhit protein clustering nucleotide clustering
7.0 years ago by bitpir ▴ 250
1
vote
3
replies
2.5k
views
how to concatenate contigs from repseq?
refseq concatenate ncbi
updated 7.2 years ago by 35k • written 7.2 years ago by ▴ 250
0
votes
1
reply
1.1k
views
tools/resources on mixed-integer programming
probability mixed-integer programming
updated 7.2 years ago by 45k • written 7.2 years ago by ▴ 250
0
votes
1
reply
1.2k
views
taxa identification using signature vs alignment to refseq
alignment signatures refseq metagenomics
7.3 years ago by bitpir ▴ 250
1
vote
1
reply
1.9k
views
finding secondary taxid using ete3 ncbiTaxa
ete3 python ncbiTaxa taxonomyid
7.3 years ago by bitpir ▴ 250
1
vote
1
reply
4.3k
views
difference between mapq=0 and samtools flag 0x900
samtools mapq
updated 7.4 years ago by 105k • written 7.4 years ago by ▴ 250
0
votes
6
replies
2.0k
views
getting a combination of all predicted genes
bedtools gff
updated 7.5 years ago by 36k • written 7.5 years ago by ▴ 250
2
votes
5
replies
3.4k
views
getting feature annotations for all NCBI Refseq sequences
ncbi refseq annotation CDS
updated 7.5 years ago by 154k • written 7.5 years ago by ▴ 250
2
votes
4
replies
5.3k
views
IGV tracks gene annotation
IGV gene GFF
updated 7.5 years ago by 35k • written 7.5 years ago by ▴ 250
0
votes
0
replies
1.8k
views
complete and partial ORF identification
ORF gene prediciton Glimmer Genemark
7.5 years ago by bitpir ▴ 250
0
votes
4
replies
2.7k
views
Glimmer output file
ORF prediction Glimmer3
7.6 years ago by bitpir ▴ 250
4
votes
5
replies
3.2k
views
best way to do joint genotyping
gatk joint-genotyping vcf
updated 7.7 years ago by 20 • written 7.8 years ago by ▴ 250
3
votes
2
replies
2.0k
views
how does Agilent/xGen design hybridization probes?
exome sequencing custom probes
updated 7.7 years ago by ★ 1.7k • written 7.7 years ago by ▴ 250
3
votes
12
replies
5.6k
views
do blast search using gi numbers
blast
8.3 years ago by bitpir ▴ 250
4
votes
3
replies
8.5k
views
ncbi error C++ exception
blast ncbi
8.3 years ago by bitpir ▴ 250
0
votes
0
replies
2.5k
views
finding NCBI protein ID and associated COG ID
blastx nr database COG
8.3 years ago by bitpir ▴ 250
4
votes
3
replies
2.1k
views
customize reference genome
DNA-seq
updated 8.3 years ago by 48k • written 8.3 years ago by ▴ 250
0
votes
0
replies
1.2k
views
software recommendations for identifying self from non-self dna sequences
forensics dna sequencing
8.4 years ago by bitpir ▴ 250
2
votes
1
reply
1.6k
views
CNVkit plotting tumor + healthy individuals
CNVkit software
updated 8.8 years ago by ★ 2.9k • written 9.5 years ago by ▴ 250
1
vote
4
replies
3.6k
views
Question about GATK hardfiltering conditions
gatk hardfiltering
updated 8.8 years ago by 20k • written 8.8 years ago by ▴ 250
0
votes
3
replies
2.1k
views
Total SNP calculation using command line vs picardtools
picardtools SNP
updated 9.2 years ago by 13k • written 9.2 years ago by ▴ 250
6
votes
17
replies
5.4k
views
fold enrichment calculation for exome sequencing
exome fold enrichment
9.2 years ago by bitpir ▴ 250
1
vote
2
replies
11k
views
samtools counting unique mapped reads
samtools read counts
updated 3.7 years ago by • 0 • written 9.3 years ago by ▴ 250
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