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questions
2
votes
1
reply
2.1k
views
Calling SNPs on Bisulphite Data
bissnp
GATK
updated 2.1 years ago by
Ram
44k • written 8.7 years ago by
John
13k
7
votes
6
replies
2.6k
views
Is there an authoritative source for optional BAM tags?
BAM
Duplicates
MarkDuplicates
Picard
updated 6.0 years ago by
Ram
44k • written 8.5 years ago by
John
13k
11
votes
6
replies
2.8k
views
In-place writable BAM files
bgzip
bam
updated 7.1 years ago by
Biostar
20 • written 8.5 years ago by
John
13k
6
votes
5
replies
1.9k
views
Where is the BigWig Supplementary Information?
bigwig
updated 7.5 years ago by
h.mon
35k • written 7.5 years ago by
John
13k
12
votes
10
replies
3.1k
views
7 follow
SAM / BAM alignments
SAM
BAM
7.7 years ago by
John
13k
3
votes
4
replies
1.3k
views
Are they're any sequencing file formats that are fragment-centric?
sam
bam
fastq
fasta
7.8 years ago by
John
13k
4
votes
6
replies
3.4k
views
Pysam under pypy?
pysam
python
pypy
updated 2.3 years ago by
Ram
44k • written 9.5 years ago by
John
13k
6
votes
2
replies
3.3k
views
GC bias correction deepTools2
deeptools
deeptools2
updated 8.3 years ago by
Devon Ryan
104k • written 8.3 years ago by
John
13k
4
votes
5
replies
1.9k
views
Byte-wise difference between two BAMs - i.e. binary patches
BAM
updated 8.4 years ago by
Biostar
20 • written 8.4 years ago by
John
13k
1
vote
2
replies
1.8k
views
Normalization and other ambiguous terminology
normalization
updated 17 months ago by
Ram
44k • written 8.4 years ago by
John
13k
1
vote
5
replies
2.4k
views
RGID mismatch after using MergeBamAlignment
bwa-meth
picard
MergeBamAlignment
8.4 years ago by
John
13k
7
votes
8
replies
3.0k
views
How do tools parse the QNAME?
BAM
updated 8.4 years ago by
Devon Ryan
104k • written 8.4 years ago by
John
13k
4
votes
11
replies
2.7k
views
Bismark returning alignments with no chromosome, Picard not happy.
Bismark
Picard
8.5 years ago by
John
13k
6
votes
3
replies
5.5k
views
Check BAMs are complete and clean
BAM
updated 2.1 years ago by
Ram
44k • written 8.5 years ago by
John
13k
16
votes
9
replies
8.6k
views
Genomic Coverage - Samtool's undocumented "depth" verses the poorly documented pileup.
samtools
pileup
mpileup
depth
coverage
updated 2.1 years ago by
Ram
44k • written 10.1 years ago by
John
13k
10
votes
9
replies
2.9k
views
Large difference in mapping times for ChIP data
ChIP-Seq
BWA
updated 2.1 years ago by
Ram
44k • written 8.6 years ago by
John
13k
31
votes
21
replies
5.0k
views
Job Manager to parallelize otherwise consecutive bash scripts..?
parallel
xargs
bash
updated 2.1 years ago by
Ram
44k • written 8.6 years ago by
John
13k
4
votes
7
replies
2.7k
views
Identify sequencing adaptor contamination programatically
FastQC
Illumina
sequencing
updated 8.6 years ago by
harold.smith.tarheel
★ 4.9k • written 8.6 years ago by
John
13k
2
votes
2
replies
2.0k
views
Visualization of DNA composition
sequencing
seq
updated 2.1 years ago by
Ram
44k • written 8.8 years ago by
John
13k
39
votes
38
replies
9.7k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 2.1 years ago by
Ram
44k • written 8.8 years ago by
John
13k
5
votes
10
replies
5.6k
views
Antisense transcription - how to detect it?
RNA-Seq
antisense
updated 2.0 years ago by
Ram
44k • written 8.9 years ago by
John
13k
6
votes
2
replies
1.9k
views
Periodicity in SNP calling quality - is this normal?
RNA-Seq
VCF
GATK
SNP
updated 24 months ago by
Ram
44k • written 8.9 years ago by
John
13k
5
votes
6
replies
3.7k
views
GATK on RNASeq/ChIP data - distinction between no SNP and no data.
RNA-Seq
GATK
SNP
ChIP-Seq
updated 24 months ago by
Ram
44k • written 8.9 years ago by
John
13k
3
votes
2
replies
2.7k
views
Creating neo4j graph databases from UCSC tables browser
neo4j
graph-database
updated 19 months ago by
Ram
44k • written 9.3 years ago by
John
13k
10
votes
10
replies
4.7k
views
How many ways a read pair can be mapped?
sequencing
mapping
next-gen
alignment
updated 22 months ago by
Ram
44k • written 9.8 years ago by
John
13k
4
votes
2
replies
2.7k
views
Signal Distribution Charts
ChIP-Seq
next-gen
R
updated 19 months ago by
Ram
44k • written 9.3 years ago by
John
13k
7
votes
6
replies
4.8k
views
Who/What Determines The Sense And Antisense Strand
dna
sequencing
mapping
strand
strand
updated 11.4 years ago by
swbarnes2
14k • written 11.4 years ago by
John
13k
27 results • Page
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