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72
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Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 6 months ago by 55k • written 6.3 years ago by 16k
2
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1
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2.3k
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Answer: Answer: Convert all fasta files in one folder
3.2 years ago by finswimmer 16k
1
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0
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1.2k
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Answer: Answer: How to extract reads which contain specific sequence from pair-end fastq files
3.3 years ago by finswimmer 16k
3
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0
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1.9k
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Answer: Answer: Use bcftools to find carriers of variants
3.3 years ago by finswimmer 16k
1
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0
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1.9k
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Answer: Answer: Both bcftools norm and vt normalization failing for the same variant?
3.4 years ago by finswimmer 16k
0
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0
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1.2k
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Comment: Comment: Removing headlines in fasta file in python
3.8 years ago by finswimmer 16k
17
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10
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7.9k
views
10 follow
Forum: Linearize fasta files
fasta code-golf
updated 3.8 years ago by ▴ 80 • written 6.3 years ago by 16k
0
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0
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1.6k
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Comment: Comment: Many TLENs in a SAM file seem much too big
4.0 years ago by finswimmer 16k
0
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0
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1.0k
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Comment: Comment: Different answers code
4.1 years ago by finswimmer 16k
0
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0
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1.5k
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Comment: Comment: How can I revert back the ensemble vep annotated positions to vcf positions?
4.2 years ago by finswimmer 16k
0
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1
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1.3k
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Comment: Comment: so any method to remove header part of FASTA file
4.2 years ago by finswimmer 16k
2
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2
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3.2k
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Answer: Answer: Excluding variants with a "LowQual" filter in bcftools consensus
4.2 years ago by finswimmer 16k
0
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1
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1.9k
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Comment: C: how to unique a file row-wise?
4.4 years ago by finswimmer 16k
0
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1
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8.9k
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Comment: C: Confused about how to generate a consensus sequence after bwa
4.4 years ago by finswimmer 16k
1
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0
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3.2k
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Answer: A: bcftools missing most indels in variant calling
4.5 years ago by finswimmer 16k
3
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0
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6.1k
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Answer: C: Sanger sequencing Result: Difference between forward and reverse DNA strands
4.5 years ago by finswimmer 16k
0
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1
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1.4k
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Comment: C: how to parse a genome "start point to end point" and find what genes inside?
4.5 years ago by finswimmer 16k
0
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0
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2.3k
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Answer: A: Freebayes - not detecting some ALT alleles
4.5 years ago by finswimmer 16k
3
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0
replies
5.0k
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Answer: C: Best ubuntu version for bioinformatics?
4.5 years ago by finswimmer 16k
106
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6
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30k
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6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 2.3 years ago by 45k • written 6.8 years ago by 16k
0
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1
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3.3k
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Comment: C: convert TCGA hg38 maf to hg 19 maf
4.6 years ago by finswimmer 16k
0
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1
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1.3k
views
Comment: C: FASTA file header
4.6 years ago by finswimmer 16k
1
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1
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3.3k
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Answer: A: I have more reads after extracting those that are mapped...
4.6 years ago by finswimmer 16k
11
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6
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6.7k
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Converting MNP to SNP
vcf SNP freebayes
updated 3.0 years ago by ▴ 10 • written 7.6 years ago by 16k
0
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1
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1.9k
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Comment: C: SeqIO error: local variable 'qual' referenced before assignment
4.8 years ago by finswimmer 16k
2
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1
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964
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Comment: C: Exome data analysis
4.9 years ago by finswimmer 16k
0
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1
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2.2k
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Comment: C: Doing an operation on one huge VCF, use Python or would C be faster (somewhat ni
5.1 years ago by finswimmer 16k
0
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2
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2.1k
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Comment: C: gnoMAD specific mutation allele position in gnoMAD
5.1 years ago by finswimmer 16k
1
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1
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2.1k
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Comment: C: gnoMAD specific mutation allele position in gnoMAD
5.1 years ago by finswimmer 16k
1
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1
reply
2.1k
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Answer: A: gnoMAD specific mutation allele position in gnoMAD
5.1 years ago by finswimmer 16k
0
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1
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2.5k
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Comment: C: Merge vcf files with bcftools
5.1 years ago by finswimmer 16k
0
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1
reply
2.5k
views
Comment: C: Merge vcf files with bcftools
5.1 years ago by finswimmer 16k
1
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1
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2.1k
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Answer: A: Why Samtools view don't extract sequence out of the given region?
5.2 years ago by finswimmer 16k
0
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0
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2.7k
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Answer: A: Soft filtering of SNPs in a list
5.2 years ago by finswimmer 16k
1
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1
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1.3k
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Comment: C: why GATK and BCFTOOLS output different number of DP
5.2 years ago by finswimmer 16k
0
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1
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2.0k
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Comment: C: GATK4 HaplotypeCaller - read is malformed
5.2 years ago by finswimmer 16k
0
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1
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2.8k
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Comment: C: Faster filtering of vcfs using split-vep over filter_vep
5.3 years ago by finswimmer 16k
1
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0
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6.3k
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Answer: A: Alternative Depth (AD) field in VCF created with samtools mpileup and bcftools c
5.3 years ago by finswimmer 16k
2
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1
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3.4k
views
Answer: A: sed (or similar) command to remove part of the FORMAT from a vcf file?
5.3 years ago by finswimmer 16k
3
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1
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3.7k
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Answer: C: bcftools DP filtering and recode as vcftools, but for polyploids?
5.3 years ago by finswimmer 16k
2
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0
replies
6.4k
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Answer: A: Changing Sample Names in Merged VCF file
5.3 years ago by finswimmer 16k
3
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0
replies
39k
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Comment: C: Sort VCF File by Position?
5.3 years ago by finswimmer 16k
0
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1
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5.4k
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Comment: C: Slice multiple sequences with Biopython>SeqIO from fasta file - AttributeError:
5.4 years ago by finswimmer 16k
2
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1
reply
10.0k
views
Comment: C: how to remove duplicate SNP rows in vcf using bcftools norm
5.4 years ago by finswimmer 16k
0
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1
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10.0k
views
Answer: C: how to remove duplicate SNP rows in vcf using bcftools norm
5.4 years ago by finswimmer 16k
1
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0
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1.6k
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Comment: C: Fasta file not matching VCF
5.4 years ago by finswimmer 16k
0
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0
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1.7k
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Comment: C: Break_blocks conversion of gvcf -> vcf
5.4 years ago by finswimmer 16k
1
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1
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1.3k
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Comment: C: How to map the first part of a read and ignoring the rest of it?
5.4 years ago by finswimmer 16k
0
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0
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1.3k
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Comment: C: How to establish a new annotation library in snpEff
5.5 years ago by finswimmer 16k
2
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0
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1.7k
views
Answer: A: What does "hfs" or "efs" stand for in amino acid changes?
5.5 years ago by finswimmer 16k
1,610 results • Page 1 of 33
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