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2
votes
6
replies
1.0k
views
Illumina reads clipped at the expected Cas9 double-strand break site – how to interpret?
illumina cas9 sequencing crispr miseq
updated 22 months ago by 141k • written 22 months ago by ▴ 80
7
votes
4
replies
897
views
How to extract variants falling in a genomic window from a VCF?
vcf
updated 2.8 years ago by 141k • written 2.8 years ago by ▴ 80
0
votes
5
replies
865
views
How can I drop the MAPQ info of my sam/bam file?
bam
updated 2.9 years ago by 8.7k • written 2.9 years ago by ▴ 80
2
votes
4
replies
1.1k
views
Rsamtools: get nucleotide of read ID X at position P
rsamtools
2.9 years ago by francois ▴ 80
4
votes
1
reply
903
views
How to trim alignments in a BAM file to a restricted genomic window?
bam alignment
updated 3.0 years ago by 161k • written 3.0 years ago by ▴ 80
8
votes
16
replies
4.4k
views
bedtools bamtofastq generates fastq which cannot be gzip correctly?
gzip miseq bedtools fastq bamtofastq
updated 3.1 years ago by 100k • written 3.1 years ago by ▴ 80
0
votes
2
replies
1.4k
views
Why does samtools calmd change the NM tag when generating the MD tag?
sequencing
3.8 years ago by francois ▴ 80
3
votes
2
replies
1.2k
views
How to report coverage at overlapping regions of paired-end reads?
illumina paired-end
updated 4.3 years ago by 35k • written 4.3 years ago by ▴ 80
6
votes
5
replies
3.3k
views
biomaRt: Cannot access the zebra fish dataset
biomart r
updated 4.6 years ago by ▴ 90 • written 6.4 years ago by ▴ 80
0
votes
2
replies
1.5k
views
No reads in IGV at the positions indicated by the bed file
sequencing
4.9 years ago by francois ▴ 80
2
votes
8
replies
1.3k
views
RNAseq: What's the accurate way to test whether a set of N genes is differentially expressed?
RNA-Seq
updated 5.0 years ago by 104k • written 5.0 years ago by ▴ 80
2
votes
2
replies
778
views
Can I conclude anything from MiSeq primer reads?
sequencing
updated 5.0 years ago by 8.9k • written 5.0 years ago by ▴ 80
2
votes
8
replies
1.5k
views
How to predict non-sense mediated decay from Illumina reads?
sequencing
5.1 years ago by francois ▴ 80
6
votes
3
replies
3.6k
views
Why do I have more reads in my .bam file than in my .fastq input file?
alignment bam fastq
updated 5.8 years ago by 161k • written 5.8 years ago by ▴ 80
0
votes
2
replies
1.5k
views
Can IGV tell me where to look?
igv nanopore minion
5.8 years ago by francois ▴ 80
3
votes
6
replies
1.9k
views
IGV not highlighting possible variants
igv
updated 5.9 years ago by 141k • written 5.9 years ago by ▴ 80
6
votes
7
replies
3.8k
views
Where are my reads in IGV?
igv alignment
5.9 years ago by francois ▴ 80
6
votes
11
replies
5.2k
views
"Invalid BAM file header: missing sequence name in file" when trying to visualise .bam file in IGV
alignment bam igv
updated 5.9 years ago by 47k • written 5.9 years ago by ▴ 80
6
votes
4
replies
1.4k
views
Why GWASs cannot speculate what kind of mutation the SNP would cause?
gwas SNP
updated 6.2 years ago by ▴ 600 • written 6.2 years ago by ▴ 80
0
votes
5
replies
3.0k
views
R: How to loop to extract all sequences within specific positions?
R sequence
updated 6.7 years ago by • 0 • written 7.4 years ago by ▴ 80
0
votes
0
replies
1.0k
views
How should I use year dates in GDAC clinical data?
tcga cancer
6.9 years ago by francois ▴ 80
4
votes
6
replies
5.2k
views
With Python, how can I solve this restriction mapping problem?
python restriction
7.2 years ago by francois ▴ 80
2
votes
3
replies
2.0k
views
R: How to correctly compute p-value of a k-mer?
R genome motif
updated 7.4 years ago by ★ 1.8k • written 7.4 years ago by ▴ 80
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