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Kamil S Jaron's user avatar
Kamil S Jaron's user avatar
Kamil S Jaron's user avatar
Kamil S Jaron
  • Member for 7 years, 1 month
  • Last seen more than a week ago
35 votes
2 answers
3k views

Why do some assemblers require an odd-length kmer for the construction of de Bruijn graphs?

21 votes
10 answers
7k views

What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?

19 votes
3 answers
698 views

How to deal with heterozygosity during polishing of genome assembly based on long reads?

17 votes
5 answers
11k views

Is there an easy way to create a summary of a VCF file (v4.1) with structural variations?

15 votes
2 answers
446 views

How can I call structural variants (SVs) from pair-end short read resequencing data?

13 votes
1 answer
188 views

Is it possible to use SNP heterozygosity as a proxy for Indel heterozygosity?

10 votes
2 answers
8k views

How to resolve in snakemake error : "Target rules may not contain wildcards."

8 votes
3 answers
4k views

How to merge sam files together with adding read groups

8 votes
4 answers
2k views

Is there a point in recalibration of scores for variant calling?

7 votes
1 answer
3k views

Index a BAM file using pysam

6 votes
2 answers
1k views

How to safely and efficiently convert subset of bam to fastq?

6 votes
2 answers
1k views

How to achieve blast results according to the intuitive interpretation of `-max_target_seqs`?

5 votes
2 answers
724 views

A reliable fetcher of short read using SRA/ENA accession

5 votes
2 answers
866 views

What does "fetching by region is not available for SAM files" mean?

4 votes
3 answers
2k views

How to specify resources for cluster in snakemake

3 votes
2 answers
496 views

mapping heteryzygous kmers on a genome

3 votes
1 answer
620 views

python does not quit when the input file is too big

3 votes
1 answer
710 views

using snakemake shadow rules to store temp files on local nodes

3 votes
2 answers
602 views

What happened to sra ftp server?

2 votes
2 answers
2k views

How to convert fasta alignment to nexus or phylip format?

2 votes
0 answers
38 views

Is there a risk in inference of structural variations using mate-pairs?

1 vote
0 answers
145 views

Colinearity analysis with respect to gene orientation

1 vote
0 answers
304 views

How to rename Read Groups

1 vote
1 answer
167 views

freebayes segmentation fault

1 vote
2 answers
77 views

How to specify the list of contigs in AGP gap file used for ENA submissions

1 vote
2 answers
380 views

How to convert CRAM file with 10x data in three fastq files

1 vote
1 answer
485 views

Quality GL entries in vcf file

1 vote
1 answer
67 views

What is the per-gene score in BUSCO output?

1 vote
1 answer
600 views

Getting sequences of one transcript per gene out of annotation and genome

0 votes
1 answer
74 views

how to get FlyBase ID conversion table