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Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 11 weeks ago by ★ 1.2k • written 5.2 years ago by 16k
2
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1
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1.6k
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Answer: Answer: Convert all fasta files in one folder
2.1 years ago by finswimmer 16k
1
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0
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736
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Answer: Answer: How to extract reads which contain specific sequence from pair-end fastq files
2.3 years ago by finswimmer 16k
3
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0
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1.2k
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Answer: Answer: Use bcftools to find carriers of variants
2.3 years ago by finswimmer 16k
1
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0
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1.2k
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Answer: Answer: Both bcftools norm and vt normalization failing for the same variant?
2.4 years ago by finswimmer 16k
0
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0
replies
802
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Comment: Comment: Removing headlines in fasta file in python
2.7 years ago by finswimmer 16k
17
votes
10
replies
6.6k
views
10 follow
Forum: Linearize fasta files
fasta code-golf
updated 2.8 years ago by ▴ 80 • written 5.3 years ago by 16k
0
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0
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1.2k
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Comment: Comment: Many TLENs in a SAM file seem much too big
2.9 years ago by finswimmer 16k
0
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0
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698
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Comment: Comment: Different answers code
3.1 years ago by finswimmer 16k
0
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0
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1.0k
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Comment: Comment: How can I revert back the ensemble vep annotated positions to vcf positions?
3.1 years ago by finswimmer 16k
0
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1
reply
988
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Comment: Comment: so any method to remove header part of FASTA file
3.2 years ago by finswimmer 16k
2
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2
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2.5k
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Answer: Answer: Excluding variants with a "LowQual" filter in bcftools consensus
3.2 years ago by finswimmer 16k
0
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1
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1.3k
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Comment: C: how to unique a file row-wise?
3.4 years ago by finswimmer 16k
0
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1
reply
7.4k
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Comment: C: Confused about how to generate a consensus sequence after bwa
3.4 years ago by finswimmer 16k
1
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0
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2.5k
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Answer: A: bcftools missing most indels in variant calling
3.4 years ago by finswimmer 16k
3
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0
replies
5.0k
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Answer: C: Sanger sequencing Result: Difference between forward and reverse DNA strands
3.4 years ago by finswimmer 16k
0
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1
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1.1k
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Comment: C: how to parse a genome "start point to end point" and find what genes inside?
3.4 years ago by finswimmer 16k
0
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0
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1.6k
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Answer: A: Freebayes - not detecting some ALT alleles
3.5 years ago by finswimmer 16k
3
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0
replies
3.4k
views
Answer: C: Best ubuntu version for bioinformatics?
3.5 years ago by finswimmer 16k
106
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6
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26k
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6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 14 months ago by 44k • written 5.7 years ago by 16k
0
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1
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2.5k
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Comment: C: convert TCGA hg38 maf to hg 19 maf
3.6 years ago by finswimmer 16k
0
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1
reply
904
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Comment: C: FASTA file header
3.6 years ago by finswimmer 16k
1
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1
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2.1k
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Answer: A: I have more reads after extracting those that are mapped...
3.6 years ago by finswimmer 16k
11
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6
replies
5.7k
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Converting MNP to SNP
vcf SNP freebayes
updated 23 months ago by ▴ 10 • written 6.6 years ago by 16k
0
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1
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1.4k
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Comment: C: SeqIO error: local variable 'qual' referenced before assignment
3.8 years ago by finswimmer 16k
2
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1
reply
673
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Comment: C: Exome data analysis
3.9 years ago by finswimmer 16k
0
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1
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1.6k
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Comment: C: Doing an operation on one huge VCF, use Python or would C be faster (somewhat ni
4.0 years ago by finswimmer 16k
0
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2
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1.3k
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Comment: C: gnoMAD specific mutation allele position in gnoMAD
4.0 years ago by finswimmer 16k
1
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1
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1.3k
views
Comment: C: gnoMAD specific mutation allele position in gnoMAD
4.0 years ago by finswimmer 16k
1
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1
reply
1.3k
views
Answer: A: gnoMAD specific mutation allele position in gnoMAD
4.0 years ago by finswimmer 16k
0
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1
reply
1.9k
views
Comment: C: Merge vcf files with bcftools
4.1 years ago by finswimmer 16k
0
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1
reply
1.9k
views
Comment: C: Merge vcf files with bcftools
4.1 years ago by finswimmer 16k
1
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1
reply
1.7k
views
Answer: A: Why Samtools view don't extract sequence out of the given region?
4.1 years ago by finswimmer 16k
0
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0
replies
2.1k
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Answer: A: Soft filtering of SNPs in a list
4.1 years ago by finswimmer 16k
1
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1
reply
904
views
Comment: C: why GATK and BCFTOOLS output different number of DP
4.1 years ago by finswimmer 16k
0
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1
reply
1.5k
views
Comment: C: GATK4 HaplotypeCaller - read is malformed
4.2 years ago by finswimmer 16k
0
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1
reply
2.3k
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Comment: C: Faster filtering of vcfs using split-vep over filter_vep
4.2 years ago by finswimmer 16k
0
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0
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4.8k
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Answer: A: Alternative Depth (AD) field in VCF created with samtools mpileup and bcftools c
4.2 years ago by finswimmer 16k
2
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1
reply
2.4k
views
Answer: A: sed (or similar) command to remove part of the FORMAT from a vcf file?
4.3 years ago by finswimmer 16k
3
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1
reply
3.0k
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Answer: C: bcftools DP filtering and recode as vcftools, but for polyploids?
4.3 years ago by finswimmer 16k
2
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0
replies
5.3k
views
Answer: A: Changing Sample Names in Merged VCF file
4.3 years ago by finswimmer 16k
3
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0
replies
33k
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Comment: C: Sort VCF File by Position?
4.3 years ago by finswimmer 16k
0
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1
reply
4.5k
views
Comment: C: Slice multiple sequences with Biopython>SeqIO from fasta file - AttributeError:
4.3 years ago by finswimmer 16k
2
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1
reply
7.6k
views
Comment: C: how to remove duplicate SNP rows in vcf using bcftools norm
4.3 years ago by finswimmer 16k
0
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1
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7.6k
views
Answer: C: how to remove duplicate SNP rows in vcf using bcftools norm
4.3 years ago by finswimmer 16k
1
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0
replies
1.1k
views
Comment: C: Fasta file not matching VCF
4.3 years ago by finswimmer 16k
0
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0
replies
1.4k
views
Comment: C: Break_blocks conversion of gvcf -> vcf
4.4 years ago by finswimmer 16k
1
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1
reply
964
views
Comment: C: How to map the first part of a read and ignoring the rest of it?
4.4 years ago by finswimmer 16k
0
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0
replies
1.1k
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Comment: C: How to establish a new annotation library in snpEff
4.4 years ago by finswimmer 16k
2
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0
replies
1.2k
views
Answer: A: What does "hfs" or "efs" stand for in amino acid changes?
4.5 years ago by finswimmer 16k
1,610 results • Page 1 of 33
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