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802
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Do we have any disease specific SNVs database?
cancer mutation SNP SNV database
updated 2.1 years ago by 9.8k • written 2.1 years ago by • 0
1
vote
2
replies
765
views
How should I interpret FB_Plot in microarray analysis?
microarray analysis control quality
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
6
replies
1.4k
views
zero byte files in sratoolkit.3.0.1-ubuntu64
fastq sra-toolkit rna-seq
updated 2.2 years ago by • 0 • written 2.2 years ago by • 0
7
votes
4
replies
1.3k
views
Processed RNA seq data publicly available
RNA-seq
updated 2.1 years ago by 45k • written 2.2 years ago by • 0
0
votes
3
replies
1.1k
views
Combining multiple datasets increases the fgsea p-value
enrichment fgsea dataset
updated 2.3 years ago by ★ 2.0k • written 2.3 years ago by • 0
0
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0
replies
1.1k
views
Comment: Comment: Combining multiple datasets increases the fgsea p-value
2.3 years ago by Nemo • 0
0
votes
1
reply
894
views
Comment: Comment: What is the default/best practice to map prob IDs to gene IDs
2.3 years ago by Nemo • 0
2
votes
3
replies
894
views
What is the default/best practice to map prob IDs to gene IDs
gsea map gene prob
updated 2.3 years ago by ★ 2.4k • written 2.3 years ago by • 0
2
votes
2
replies
851
views
Question regarding pathways and cell types
signaling types cell pathway
updated 2.3 years ago by 4.6k • written 2.3 years ago by • 0
0
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0
replies
892
views
Comment: Comment: predict gain/ loss of function from mutation
2.4 years ago by Nemo • 0
0
votes
1
reply
892
views
Comment: Comment: predict gain/ loss of function from mutation
2.4 years ago by Nemo • 0
0
votes
3
replies
892
views
predict gain/ loss of function from mutation
protein mutation loss gain
2.4 years ago by Nemo • 0
2
votes
1
reply
754
views
Get variant type from genotype data
type missense mutation nonsense variant
updated 2.4 years ago by ★ 4.8k • written 2.4 years ago by • 0
0
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1
reply
1.1k
views
Comment: Comment: Htseq-count output file having a high number of __not_aligned
2.5 years ago by Nemo • 0
0
votes
3
replies
1.1k
views
Htseq-count output file having a high number of __not_aligned
read htseq-count human counts genome alignment
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by • 0
0
votes
0
replies
404
views
The region for RNase P gene in human genome
gene genome read count
2.5 years ago by Nemo • 0
0
votes
1
reply
612
views
How parse collectReadCounts output in r?
CollectReadCounts r gatk rstudio
updated 2.5 years ago by 102k • written 2.5 years ago by • 0
0
votes
0
replies
1.1k
views
Comment: Comment: Get distribution of enrichment scores across all permutations in fgsea
2.5 years ago by Nemo • 0
3
votes
1
reply
659
views
aligning RNA seq data against human genome
variant calling rna-seq alignment
updated 2.5 years ago by 150k • written 2.5 years ago by • 0
0
votes
1
reply
1.1k
views
Comment: Comment: Get distribution of enrichment scores across all permutations in fgsea
2.5 years ago by Nemo • 0
0
votes
3
replies
1.1k
views
Get distribution of enrichment scores across all permutations in fgsea
enrichment gsea pathway analysis fgsea permutation
2.5 years ago by Nemo • 0
0
votes
1
reply
746
views
Normalizing read counts while having multiple group of samples with different conditions
FPKM normalizing rna-seq read-count alignment
updated 2.6 years ago by 11k • written 2.6 years ago by • 0
0
votes
0
replies
665
views
Comment: Comment: Normalized read counts with FPKM
2.6 years ago by Nemo • 0
0
votes
1
reply
665
views
Normalized read counts with FPKM
Read FPKM Normalize count RNA-Sequnce
2.6 years ago by Nemo • 0
0
votes
1
reply
820
views
Comment: Comment: How can I get the number of reads per variant in hisat2?
2.6 years ago by Nemo • 0
1
vote
3
replies
820
views
How can I get the number of reads per variant in hisat2?
alignemnt variant gatk covid hisat2
updated 2.6 years ago by 3.3k • written 2.6 years ago by • 0
0
votes
1
reply
903
views
Comment: Comment: What is chrom and position values in Wuhan-Hu-1 genome data
2.6 years ago by Nemo • 0
2
votes
3
replies
903
views
What is chrom and position values in Wuhan-Hu-1 genome data
alignemnt variant gatk covid hisat2
updated 2.6 years ago by 150k • written 2.6 years ago by • 0
0
votes
0
replies
1.1k
views
Comment: Comment: Why there are variants of covid (delta and omicron) in normal samples?
2.6 years ago by Nemo • 0
0
votes
1
reply
1.1k
views
Comment: Comment: Why there are variants of covid (delta and omicron) in normal samples?
2.6 years ago by Nemo • 0
0
votes
1
reply
1.1k
views
Comment: Comment: Why there are variants of covid (delta and omicron) in normal samples?
2.6 years ago by Nemo • 0
1
vote
6
replies
1.1k
views
Why there are variants of covid (delta and omicron) in normal samples?
alignemnt variant gatk covid hisat2
2.6 years ago by Nemo • 0
0
votes
1
reply
1.7k
views
Comment: Comment: What is --known-sites in BaseRecalibration of GATK
2.6 years ago by Nemo • 0
0
votes
1
reply
1.7k
views
Comment: Comment: What is --known-sites in BaseRecalibration of GATK
2.6 years ago by Nemo • 0
0
votes
5
replies
1.7k
views
What is --known-sites in BaseRecalibration of GATK
rna-seq gatk variants site baserecalibration
updated 2.6 years ago by 3.3k • written 2.6 years ago by • 0
2
votes
1
reply
1.0k
views
Can MarkDuplicates of Picard be used for RNA reads?
variants MarkDuplicates rna picard
updated 2.6 years ago by 4.9k • written 2.6 years ago by • 0
1
vote
1
reply
948
views
Problem in MarkDuplicates of picard
variants MarkDuplicates picard rna
updated 2.6 years ago by 165k • written 2.6 years ago by • 0
0
votes
1
reply
1.5k
views
Comment: Comment: using gatk haplotypecaller for variants extraction
2.6 years ago by Nemo • 0
0
votes
3
replies
1.5k
views
using gatk haplotypecaller for variants extraction
variants gatk haplotypecaller rna-seq
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
0
votes
0
replies
1.0k
views
Comment: Comment: Splice aware or not for RNA sequence data
2.6 years ago by Nemo • 0
1
vote
2
replies
1.0k
views
Splice aware or not for RNA sequence data
splice RNA hisat2 sequence alignment
2.6 years ago by Nemo • 0
0
votes
0
replies
506
views
CalibrateDragstrModel - Not enough cases to estimate parameters, using defaults
dragen-os calibration gatk dragen alignment
2.6 years ago by Nemo • 0
0
votes
0
replies
517
views
Control detected variants for normal samples in dragen
calling illumina variants dragen alignment
2.6 years ago by Nemo • 0
0
votes
9
replies
2.6k
views
Not producing sam file in hisat2
sam hisat2 header alignment
updated 2.5 years ago by ▴ 30 • written 2.6 years ago by • 0
0
votes
0
replies
2.6k
views
Answer: Answer: Not producing sam file in hisat2
2.6 years ago by Nemo • 0
0
votes
1
reply
2.6k
views
Comment: Comment: Not producing sam file in hisat2
2.6 years ago by Nemo • 0
0
votes
0
replies
2.6k
views
Comment: Comment: Not producing sam file in hisat2
2.6 years ago by Nemo • 0
0
votes
0
replies
2.1k
views
Comment: Comment: Adding @RG header line to bam and sam files in hisat2
2.6 years ago by Nemo • 0
0
votes
1
reply
2.6k
views
Comment: Comment: Not producing sam file in hisat2
2.6 years ago by Nemo • 0
0
votes
1
reply
2.1k
views
Comment: Comment: Adding @RG header line to bam and sam files in hisat2
2.6 years ago by Nemo • 0
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