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1
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2
replies
1.4k
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Where to find known sites for mm39 used by GATK4 BaseRecalibrator?
BaseRecalibrator mouse gatk
3.0 years ago by 乙 ▴ 240
24
votes
24
replies
22k
views
8 follow
bcl2fastq2: how to correctly use the --use-bases-mask for different sequencing methods by Illumina ?
bcl2fastq2 --use-bases-mask sequencing illumina
updated 3.6 years ago by ▴ 320 • written 6.5 years ago by ▴ 240
11
votes
18
replies
3.7k
views
6 follow
Is there a tool to find the correct percentage of duplication levels in FastQ ?
sequencing fastq
updated 4.8 years ago by 150k • written 4.8 years ago by ▴ 240
0
votes
2
replies
1.1k
views
Is it possible to get the Codons for an intron/splice mutation given the chromosome and position?
codons introns
4.9 years ago by 乙 ▴ 240
6
votes
5
replies
1.3k
views
Is it possible to convert NC_ to NP_ for RefSeq ?
RefSeq
5.0 years ago by 乙 ▴ 240
1
vote
0
replies
2.1k
views
What are the min/max of the MaxEntScan software ?
maxentscan
5.1 years ago by 乙 ▴ 240
1
vote
0
replies
928
views
Any changes to the frequencies of gnomAD v2.1 liftover ?
gnomAD liftovert hg19 hg38
5.2 years ago by 乙 ▴ 240
4
votes
9
replies
2.7k
views
Is it possible to obtain all the RefSeq transcripts of Ensembl genes for GRCh37 ?
Ensembl RefSeq transcripts genes
updated 5.3 years ago by 24k • written 5.3 years ago by ▴ 240
4
votes
12
replies
2.8k
views
Is it possible to output uncompressed FastQ files with bcl2fastq2 ?
decompression bcl2fastq2 fastq bcl raw
5.7 years ago by 乙 ▴ 240
13
votes
16
replies
4.6k
views
8 follow
RNA-seq: is there a way to get the variability between biological replicates ?
RNA-Seq
updated 6.1 years ago by 8.3k • written 6.1 years ago by ▴ 240
15
votes
14
replies
2.0k
views
RNA-seq: Is it worth to analyze case vs control separately to have a % similarity ?
RNA-Seq
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by ▴ 240
15
votes
3
replies
5.7k
views
What does CSQ means in a VCF file annotated by VEP ?
VCF CSQ
updated 6.1 years ago by 47k • written 6.1 years ago by ▴ 240
1
vote
3
replies
1.4k
views
MySQL: Mapping GRCh38 coordinates to GRCh37 using ensembldb
ensembl MySQL Assembly mapping
updated 6.3 years ago by 166k • written 6.3 years ago by ▴ 240
5
votes
15
replies
9.9k
views
9 follow
Using Circos plot to visualize RNA-seq data
Circos RNA-Seq visualization
updated 6.7 years ago by ★ 3.4k • written 6.8 years ago by ▴ 240
4
votes
7
replies
3.2k
views
HTSeq-count [Python] is not properly counting reads like Genomic Alignments [R] ?
RNA-Seq HTSeq-count GenomicAlignments
6.9 years ago by 乙 ▴ 240
2
votes
3
replies
3.4k
views
Overlap of variants between CaVEMan and MuTect2 ?
Whole Exome Sequencing MuTect2 CaVEMan sequencing
7.0 years ago by 乙 ▴ 240
4
votes
8
replies
4.2k
views
[solved] SnpEff reports intron variants in exons ?
SnpEff SNP Annotation Exome-seq
updated 7.6 years ago by 21k • written 7.6 years ago by ▴ 240
1
vote
0
replies
1.5k
views
CHASM vs VEST
Functional Somatic Annotation CRAVAT CHASM VEST
7.6 years ago by 乙 ▴ 240
5
votes
2
replies
3.3k
views
Intersection of a BED genes with multiple VCFs: report only if at least N intersection.
WES bedtools VCF BED Intersection
updated 7.9 years ago by 36k • written 7.9 years ago by ▴ 240
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