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488
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Get Cluster PF % and Cluster Density from Interop module using python
Interop python
4 months ago by kspata ▴ 80
0
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0
replies
656
views
bed2vcf (bedr) package error
R vcf bedr bed
updated 2.6 years ago by 161k • written 2.6 years ago by ▴ 80
0
votes
1
reply
524
views
Convert coordinates from one cotton genome to another
Genome over cotton lift
updated 2.6 years ago by 15k • written 2.6 years ago by ▴ 80
1
vote
3
replies
1.2k
views
differences between Illumina Platinum Variant Calls and NIST variant calls
SNP vcf
updated 2.6 years ago by • 0 • written 4.8 years ago by ▴ 80
3
votes
7
replies
1.5k
views
7 follow
Annotation of non model fish (mahi mahi) genome
Assembly Annotation
updated 3.1 years ago by 8.5k • written 3.8 years ago by ▴ 80
0
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0
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519
views
Total number of trimmed reads less than number of mapped reads
alignment next-gen sequence SAMtools BWA
3.1 years ago by kspata ▴ 80
0
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3
replies
1.0k
views
Extract unique barcodes and find their frequency
ngs illumina mapping
3.5 years ago by kspata ▴ 80
0
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5
replies
742
views
Read showing Insertion of 41 bases when aligned with BWA
Variant BWA Bowtie2
updated 3.8 years ago by 14k • written 3.8 years ago by ▴ 80
0
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0
replies
709
views
Detect Transgene Insertion Site using SAM format
Transgene Insertion Site BWA SAM tools
4.1 years ago by kspata ▴ 80
0
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0
replies
694
views
Comparative analysis of experimental and control data from BS seq run
BS seq CpG Annoattion Bismark
4.3 years ago by kspata ▴ 80
0
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0
replies
985
views
Calculate LOH score for tumor only sample using GenomeStudio
GenomeStudio Infinium Assay Genotyping LOH score
4.4 years ago by kspata ▴ 80
0
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10
replies
11k
views
sh: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8)
perl bash bwa
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 80
0
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2
replies
1.4k
views
Validation of SNP and INDEL calling pipeline
genome alignment SNP INDEL
updated 4.9 years ago by 47k • written 4.9 years ago by ▴ 80
1
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3
replies
1.7k
views
Find the genomic position of CTCF binding site on DMPK gene
gene genome UCSC Genome Browser
updated 4.9 years ago by 20 • written 5.9 years ago by ▴ 80
1
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0
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1.0k
views
Variant discrepancy between technical replicates
freebayes alignment
updated 5.0 years ago by 12k • written 5.0 years ago by ▴ 80
0
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0
replies
884
views
Error running samjdk.jar for extracting reads containing indels
alignment jvarkit samjdk indels
5.0 years ago by kspata ▴ 80
7
votes
10
replies
2.7k
views
Effect of trimming on alignment and fastqc report.
alignment next gen Fastqc trim galore
updated 5.1 years ago by 8.9k • written 5.1 years ago by ▴ 80
0
votes
7
replies
1.1k
views
Partially map reads to a reference genome
alignment sequencing binning
5.1 years ago by kspata ▴ 80
2
votes
7
replies
1.3k
views
Obtain sequence of a gene with vector DNA integrated
assembly gene next-gen alignment
updated 5.1 years ago by ★ 2.5k • written 5.1 years ago by ▴ 80
0
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2
replies
1.2k
views
Coverage Discrepancy for samtools mpileup
sequencing alignment Plasmid
updated 5.2 years ago by 20 • written 5.2 years ago by ▴ 80
0
votes
10
replies
1.4k
views
Identification and taxonomic classification of Nematode
next-gen PCR products Nematode 18S
5.2 years ago by kspata ▴ 80
1
vote
1
reply
1.3k
views
Low % Phred Q30 for one of the lanes in HiSeq 4000 SE50 run
sequencing ChIP-Seq Barcode
updated 5.2 years ago by 141k • written 5.2 years ago by ▴ 80
0
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2
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1.6k
views
Set minimum variant frequency while calling variants with samtools
samtools resequencing alignment variant frequency
updated 5.2 years ago by 100k • written 5.2 years ago by ▴ 80
1
vote
1
reply
2.4k
views
Remove low quality base calls from reads
Trimming Trim_Galore Alignment Variant Calls
updated 5.2 years ago by ★ 1.3k • written 5.2 years ago by ▴ 80
3
votes
2
replies
1.2k
views
Audit trail for Bioinformatics software tools
next-gen align samtools alignment
updated 5.3 years ago by 20 • written 5.3 years ago by ▴ 80
0
votes
0
replies
887
views
Identify RNA and non-AAV vector molecules in a sample
assembly alignment contamination
5.3 years ago by kspata ▴ 80
1
vote
3
replies
1.6k
views
PhiX forward and reverse reads for MiSeq and NextSeq Platform
sequencing next-gen Illumina
5.3 years ago by kspata ▴ 80
0
votes
3
replies
1.2k
views
Error in parsing BAM file using readAlligned
R alignment gene
updated 5.4 years ago by 14k • written 5.4 years ago by ▴ 80
0
votes
1
reply
2.3k
views
Merge Samtools and Freebayes vcf files
alignment exome variants
updated 5.4 years ago by 161k • written 5.4 years ago by ▴ 80
0
votes
4
replies
1.3k
views
Missing sequence from a cosmid de novo assembly
assembly spades de novo sequencing
updated 5.4 years ago by ★ 4.9k • written 5.4 years ago by ▴ 80
1
vote
4
replies
1.3k
views
Obtaining depth for all positions for different exonic ranges from mpileup file
next-gen gene resequencing exonic coverage
updated 5.4 years ago by 161k • written 5.4 years ago by ▴ 80
7
votes
2
replies
2.7k
views
Current version of human reference Genome Assembly
genome reference Assembly
updated 5.5 years ago by ★ 3.7k • written 5.5 years ago by ▴ 80
0
votes
0
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721
views
reformat forward and reverse read pairs for variant analysis of exons
assembly variant calling gene exon capture
5.5 years ago by kspata ▴ 80
1
vote
4
replies
2.2k
views
de novo assembly of circular plasmid
assembly de novo spades plasmids
updated 5.6 years ago by ★ 1.8k • written 5.6 years ago by ▴ 80
1
vote
1
reply
869
views
Strategy to detect deletions in the PE 300 reads
sequencing Assembly SNP Indels
5.6 years ago by kspata ▴ 80
2
votes
5
replies
2.4k
views
Merge multiple overlapping consensus sequences
assembly consensus
updated 5.6 years ago by 43k • written 5.8 years ago by ▴ 80
0
votes
2
replies
1.4k
views
Deletions in a consensus sequence.
alignment sequencing Deletions Consnesus Sequence
5.6 years ago by kspata ▴ 80
0
votes
0
replies
814
views
Deletion detected at less frequency than expected for a plasmid sample
alignment assembly
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 80
2
votes
3
replies
1.5k
views
Variant Allele Frequency
snp vcf samtools
updated 5.7 years ago by ▴ 300 • written 5.7 years ago by ▴ 80
1
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5
replies
1.5k
views
download genbank sequences with exon sequences highlighted
gene Genbank
updated 5.7 years ago by ▴ 370 • written 5.7 years ago by ▴ 80
0
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7
replies
1.2k
views
Low coverage for bases near the end of target reference sequence
alignment bowtie2 sequencing
5.7 years ago by kspata ▴ 80
3
votes
1
reply
1.2k
views
Base by base alignment from BLAST to reference
Blast alignment
updated 5.8 years ago by 35k • written 5.8 years ago by ▴ 80
1
vote
4
replies
2.1k
views
How to find rs numbers from Coriell ID
dbSNP 1000Genomes Coriell ID rs numbers
5.8 years ago by kspata ▴ 80
5
votes
4
replies
2.9k
views
How to know if a variant is sequencing or mapping artifact?
Variant freebayes vcf
updated 5.8 years ago by 16k • written 5.8 years ago by ▴ 80
0
votes
2
replies
2.7k
views
Generate Consensus Sequence from Pairwise Alignment
alignment Consensus Blast
5.8 years ago by kspata ▴ 80
1
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1
reply
2.0k
views
Find variants supported by at least 20 reads freebayes
Freebayes Variant Calling
updated 5.9 years ago by 16k • written 5.9 years ago by ▴ 80
0
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3
replies
1.3k
views
Mpileup generation using Bisulfite converted reference
mpileup faidx samtools bismark bisulfite
5.9 years ago by kspata ▴ 80
0
votes
0
replies
1.1k
views
Methylation Status of CpG islands for a specific gene
gene R BS methylKit Bismark
5.9 years ago by kspata ▴ 80
9
votes
13
replies
6.9k
views
Calculate Mapping Rate for an alignment to each sequence of a multi-fasta reference
RNA-Seq SAMtools flagstat bowtie2 Mapping Rate
updated 6.0 years ago by 35k • written 6.0 years ago by ▴ 80
3
votes
3
replies
3.2k
views
Convert blastn to gff3
blastp gff3 blastn gff3
7.0 years ago by kspata ▴ 80
52 results • Page 1 of 2
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