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Devon Ryan
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  • Member for 5 years, 3 months
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23 votes
Accepted

Convert a BAM file from one reference to another?

22 votes
Accepted

What is the fastest way to get the reverse complement of a DNA sequence in python?

18 votes

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

17 votes
Accepted

Why would someone use a CRAM instead of a BAM?

15 votes

Understanding DESeq2 design, contrast and results

15 votes
Accepted

Are soft-clipped bases used for variant calling in samtools + bcftools?

15 votes

How exactly is "effective length" used in FPKM calculated?

14 votes
Accepted

Merge hundreds of small BAM files into a single BAM file

13 votes

What Ensembl genome version should I use for alignments? (e.g. toplevel.fa vs. primary_assembly.fa)

13 votes
Accepted

Using the t-SNE algorithm on microarray data + an error bonus

13 votes
Accepted

Can open-source software be peer-reviewed and published?

12 votes
Accepted

Definition of "seed" in sequence alignment

12 votes
Accepted

Difference between CPM and TPM and which one for downstream analysis?

12 votes
Accepted

How can I extract normalized read count values from DESeq2 results?

12 votes

Convert bam file to highly compressible bam

10 votes
Accepted

Bootstrap analysis - why it is called bootstrap?

10 votes

How to detect a mutation and predict its consequence?

10 votes

What methods are available to find a cutoff value for non-expressed genes in RNA-seq?

10 votes
Accepted

How to count reads in bam per bed interval with bedtools

10 votes
Accepted

Determine if a gene is mitochondrial or not

10 votes

Why does the SARS-Cov2 genome has letter t

9 votes

When to account for the blacklisted genomic regions in ChIP-seq data analyses?

9 votes
Accepted

Quantifying reads mapping to multiple loci

9 votes
Accepted

Extract nanopore read ID & start times from fastq file

9 votes
Accepted

R package development: How does one automatically install Bioconductor packages upon package installation?

9 votes
Accepted

How to validate that BAMs have been downloaded correctly?

9 votes
Accepted

Running SnakeMake on cluster

9 votes

What is a simple command line tool for doing Needleman-Wunsch pair-wise alignment on the command line

8 votes
Accepted

How can I count the number of reads that support a variant in a bam file?

8 votes
Accepted

How to convert a binary matrix of gene presence or absence into a fasta sequence

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