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3
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4
replies
1.7k
views
How do we handle TPM values after converting from Ensembl to HUGO genes?
ensembl hugo tpm-calculator tpm rna-seq
updated 3.7 years ago by 102k • written 3.7 years ago by ★ 1.3k
0
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0
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1.7k
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Comment: Comment: How do we handle TPM values after converting from Ensembl to HUGO genes?
3.7 years ago by Jordan ★ 1.3k
2
votes
4
replies
3.0k
views
How are the log2 values in CNVkit .cnr files calculated?
cnvkit .cnr wgs cnv
updated 4.2 years ago by 88k • written 4.7 years ago by ★ 1.3k
4
votes
8
replies
3.3k
views
Random Variance T-Test In R?
r microarray
updated 4.2 years ago by ★ 7.7k • written 10.8 years ago by ★ 1.3k
0
votes
2
replies
2.2k
views
Error while running vcf2maf tool
vep vcf2maf variant-calling vcfs maf
4.5 years ago by Jordan ★ 1.3k
1
vote
1
reply
1.9k
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Comment: C: How do you know the best segments in cnvkit after filtering?
4.6 years ago by Jordan ★ 1.3k
2
votes
3
replies
1.9k
views
How do you know the best segments in cnvkit after filtering?
cnvkit wgs cnv
updated 4.6 years ago by ▴ 840 • written 4.6 years ago by ★ 1.3k
0
votes
6
replies
1.6k
views
The center in scatter plot generated by CNVkit looks off
cnvkit wgs scatter-plot
updated 4.7 years ago by ★ 2.9k • written 4.7 years ago by ★ 1.3k
0
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1
reply
1.6k
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Comment: C: The center in scatter plot generated by CNVkit looks off
4.7 years ago by Jordan ★ 1.3k
0
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1
reply
1.6k
views
Comment: C: The center in scatter plot generated by CNVkit looks off
4.7 years ago by Jordan ★ 1.3k
0
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0
replies
3.0k
views
Comment: C: How are the log2 values in CNVkit .cnr files calculated?
4.7 years ago by Jordan ★ 1.3k
0
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1
reply
3.4k
views
Comment: Comment: Empty SomaticSniper Output Files
updated 4.9 years ago by 44k • written 10.5 years ago by ★ 1.3k
0
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1
reply
3.0k
views
Comment: A: Convert Phred score 41 to 40
updated 4.9 years ago by 44k • written 10.5 years ago by ★ 1.3k
0
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0
replies
3.8k
views
Comment: C: Find mismatch and INDEL position
updated 4.9 years ago by 44k • written 10.5 years ago by ★ 1.3k
1
vote
0
replies
3.8k
views
Answer: A: Find mismatch and INDEL position
updated 4.9 years ago by 44k • written 10.5 years ago by ★ 1.3k
1
vote
1
reply
2.9k
views
Comment: C: csfasta malformed qualities
updated 4.9 years ago by 44k • written 10.5 years ago by ★ 1.3k
0
votes
1
reply
4.9k
views
Answer: A: tophat2 stopped at bowtie step
updated 4.9 years ago by 44k • written 10.5 years ago by ★ 1.3k
0
votes
1
reply
3.9k
views
Comment: C: Can anyone tell me the frequency percentage given by varscan2 is for individual
updated 4.9 years ago by 44k • written 10.5 years ago by ★ 1.3k
0
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1
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3.9k
views
Answer: A: Can anyone tell me the frequency percentage given by varscan2 is for individual
updated 4.9 years ago by 44k • written 10.5 years ago by ★ 1.3k
2
votes
0
replies
5.2k
views
Answer: A: Mapping statistics error from mirdeep2
updated 4.9 years ago by 44k • written 10.5 years ago by ★ 1.3k
0
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1
reply
3.4k
views
Comment: C: Empty SomaticSniper Output Files
updated 4.9 years ago by 44k • written 10.5 years ago by ★ 1.3k
0
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0
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3.7k
views
Comment: C: Need help using Shrimp2 on paired end SOLiD data.
updated 5.0 years ago by 44k • written 10.6 years ago by ★ 1.3k
1
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1
reply
3.7k
views
Answer: A: Need help using Shrimp2 on paired end SOLiD data.
updated 5.0 years ago by 44k • written 10.6 years ago by ★ 1.3k
0
votes
0
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3.7k
views
Comment: C: Need help using Shrimp2 on paired end SOLiD data.
updated 5.0 years ago by 44k • written 10.6 years ago by ★ 1.3k
2
votes
1
reply
6.1k
views
Answer: A: Filtering Bed Files By Using Bedops
updated 5.0 years ago by 44k • written 11.5 years ago by ★ 1.3k
2
votes
1
reply
1.4k
views
Creating a panel of normal from one normal sample
mutect2 panelofnormals variant-calling gatk
updated 5.0 years ago by 88k • written 5.1 years ago by ★ 1.3k
0
votes
1
reply
4.7k
views
Comment: C: Need help understanding read depth for somaticsniper vcf's
updated 5.5 years ago by 44k • written 10.4 years ago by ★ 1.3k
0
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1
reply
4.7k
views
Comment: C: Need help understanding read depth for somaticsniper vcf's
updated 5.5 years ago by 44k • written 10.4 years ago by ★ 1.3k
0
votes
1
reply
4.7k
views
Comment: C: Need help understanding read depth for somaticsniper vcf's
updated 5.5 years ago by 44k • written 10.4 years ago by ★ 1.3k
11
votes
1
reply
89k
views
Answer: A: Sequence Length Distribution From A Fastq File
updated 5.6 years ago by 44k • written 11.5 years ago by ★ 1.3k
0
votes
0
replies
4.4k
views
Comment: C: Input Error Using Varscan2.3
updated 5.9 years ago by 44k • written 10.7 years ago by ★ 1.3k
2
votes
7
replies
9.9k
views
Does Bam File Include Unmapped Reads As Well?
bam mapping read
updated 6.4 years ago by • 0 • written 11.7 years ago by ★ 1.3k
2
votes
3
replies
1.5k
views
Tools for asserting matching pairs of samples from the same patient
RNA-Seq ngs
updated 6.9 years ago by 15k • written 6.9 years ago by ★ 1.3k
0
votes
0
replies
1.5k
views
Comment: C: Tools for asserting matching pairs of samples from the same patient
6.9 years ago by Jordan ★ 1.3k
4
votes
4
replies
5.2k
views
Mapping statistics error from mirdeep2
mapper.pl RNA-Seq mirdeep2
updated 3.2 years ago by 44k • written 10.6 years ago by ★ 1.3k
2
votes
5
replies
3.0k
views
What Do Marked Reads Mean In An Xsq File?
solid read
updated 7.1 years ago by 20 • written 11.8 years ago by ★ 1.3k
61
votes
23
replies
60k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 12 months ago by ★ 1.2k • written 11.8 years ago by ★ 1.3k
4
votes
3
replies
4.8k
views
How To Get The Number Of Samples And Sample Tcga Id'S That Are Reported In Tcga For Brca?
tcga
updated 9.0 years ago by 7.6k • written 10.9 years ago by ★ 1.3k
7
votes
7
replies
6.6k
views
How To Include Biological And Technical Replicates While Using Mirdeep2 For Mirna Prediction?
mirna
updated 9.2 years ago by 20 • written 10.9 years ago by ★ 1.3k
0
votes
1
reply
13k
views
Comment: Comment: Add read group to header after samtools merge
updated 2.7 years ago by 44k • written 9.5 years ago by ★ 1.3k
0
votes
0
replies
3.0k
views
Answer: Answer: How to count novel and known splice junction reads from BAM
updated 22 months ago by 44k • written 9.6 years ago by ★ 1.3k
2
votes
0
replies
3.3k
views
Answer: A: using cufflinks when investigating differential expression
9.6 years ago by Jordan ★ 1.3k
1
vote
0
replies
4.7k
views
Comment: Comment: TCGA normalized count data of 1000 samples for DGE
updated 22 months ago by 44k • written 9.6 years ago by ★ 1.3k
1
vote
1
reply
1.9k
views
Answer: Answer: Cufflinks 0.0.7 and CummeRbound
updated 2.4 years ago by 44k • written 9.7 years ago by ★ 1.3k
0
votes
1
reply
4.8k
views
Comment: C: NOT RESETTING NORMAL error using Varscan2
10.0 years ago by Jordan ★ 1.3k
1
vote
3
replies
4.8k
views
NOT RESETTING NORMAL error using Varscan2
varscan2 variant-calling SNP somatic
updated 10.0 years ago by ★ 4.3k • written 10.0 years ago by ★ 1.3k
2
votes
1
reply
3.1k
views
Proper regex to mark duplicates using Picard tools on SOLiD data
duplicate-removal picard-tools SOLiD BAMs NGS
10.0 years ago by Jordan ★ 1.3k
1
vote
0
replies
3.1k
views
Answer: A: Proper regex to mark duplicates using Picard tools on SOLiD data
10.0 years ago by Jordan ★ 1.3k
0
votes
0
replies
8.7k
views
Comment: C: Mark Duplicates from Picard does not seem to recognize my sorted BAM files.
10.0 years ago by Jordan ★ 1.3k
9
votes
6
replies
8.7k
views
Mark Duplicates from Picard does not seem to recognize my sorted BAM files.
markduplicates samtools BAM sort picard
updated 3.2 years ago by 44k • written 10.6 years ago by ★ 1.3k
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