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• How do I compute the effective genome size?
  Several pieces of software require this parameter. Is counting the number of masked nucleotides ...
• Looking for neanderthal genomes to download
  EDIT: Since the data I'm looking for isn't available, my new question is if it's possible to conc...
• no accepted_hits.bam generated
  Hi,   I am using tophat to do map alignment for RNA-seq. There is no accepted_hits.bam file tha...
• How To Have Only Id And Sequence Printed In Output After Parse Sequences From A Fasta File
  I used this piece of biopython codes written by Eric Normandeau to parse several sequences from a...
• How To Concatenate/Merge Blast Xml Outputs?
  I process my blast (BLASTN 2.2.26+) searches through a script that divides the fasta inputs into ...
• Get coordinate of several primer fasta sequence
  I have several primers in a fasta file (20nt). What's the best way to get genom coordinate of tho...
• Combining several fasta files and gff files
  Hello, I have several fasta formatted files which I need to combine them. In addition I have few...
• Sub-Record Indexing Of Fasta Files In Python?
  Hello, I have several genomes, each spread across multiple FASTA files. Some of these files cont...
• Biopython 1.56 - Strange Behaviour Of Seqio.Parse And Seqio.Write
  Hello everybody, I'm using Biopython 1.56 compiled from source on Ubuntu 10.10 64-bit. It's a gr...
• How can I create a single file (.fasta or .phylip) containing several genomes to build a phylogeny tree
  Dear colleagues I want to build a phylogeny tree for several bacterial genomes but alignment too...
• several FASTA file to one
  hi I downloaded several FASTA files (> 200) of RNA 16S to do global alignment, so there is a...
• Grow/shrink ranges in bed file to a specified length
  Is there any tool which can make entries in `bed` file equal length? I've checked `bedtools slop...
• To Simulate Heterozygous Variations In Genome
  A bit technical question here... I want to simulate an heterozygous indel starting from a piece o...
• bwa mapping to several similar strains, restrict maximum hits?
  Hello, I want to use bwa mem or aln, to align reads to 3-5 strains of a virus. However, if a rea...
• Next gen sequencing
  Suppose If I have a dna which is sheared into pieces how can they be possibly overlap? What seque...
• Downloading SRA Reads
  I am using SRA Toolkit for SRA Reads from NCBI web page. I went through the mannual and came up...
• Help scaffolding an Illumina genome assembly with 10x reads
  Hi everyone I have a draft genome assembly constructed from a single Illumina library. I have s...
• Align Sequentially All Files In A Protein Directory
  Thank you for reading my question. I am attempting to create multiple MUSCLE alignments for thou...
• SRA File Content
  Once the SRA file from NCBI using `prefetch -c ` has been downloaded...how do I see it's contents...
• Finding Gene Symbols for Probes in Raw Data
  Dear all, I'm working on **[GSE23561][1]** dataset and **[GPL10775][2]** platform. There are *...