User: c.e.chong

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c.e.chong20
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Posts by c.e.chong

<prev • 33 results • page 1 of 4 • next >
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Comment: C: Creating a bed file from a de novo fasta file
... Thanks for your help I have a bio python script to do this now. ...
written 7 weeks ago by c.e.chong20
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Comment: C: Creating a bed file from a de novo fasta file
... I’m not sure, that’s why I’m asking if it’s possible to do this as I was told this was the file I needed! I’m not clear on what you mean by 1 and length(sequence)? Thanks ...
written 7 weeks ago by c.e.chong20
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Comment: C: Creating a bed file from a de novo fasta file
... I don't want the length of the contig just the bp number where they start and end ...
written 7 weeks ago by c.e.chong20
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Creating a bed file from a de novo fasta file
... Hi all, I need to create a bed file from my fasta files (from de novo assembled Metagenomic samples). I want the contig name in one column, then the start position and end position. Does anyone have any advice on how to do this? Thanks in advance! ...
bedtools assembly metagenomics written 7 weeks ago by c.e.chong20
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Comment: C: Ways to convert fasta to faa file for functional annotation?
... I didn't see this option!! Thank you. ...
written 4 months ago by c.e.chong20
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Ways to convert fasta to faa file for functional annotation?
... Hi All, I want to convert a multifasta file (containing the nucleotide sequences of genes from the pangenome.fa output from Roary) to an amino acid sequence file, so I can input it into eggNOG-mapper to functionally annotate COGs. Does anyone know a good way to do this? Thank you in advance! ...
assembly pangenome roary annotation written 4 months ago by c.e.chong20 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: How to generate Artemis ACT comparison file of multiple sequence alignment
... Thank you very much for your help! This makes so much sense now ...
written 9 months ago by c.e.chong20
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Comment: C: How to generate Artemis ACT comparison file of multiple sequence alignment
... Hi all, I tried to use this script for to compare two fasta files that contain around 60 contigs each. When I input this into ACT I only seem to get similarity information for the first contig? Both fasta files are the same bacterial species so expected to be pretty similar. Do you have any advi ...
written 9 months ago by c.e.chong20
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Comment: C: Bowtie database of all bacterial and fungal complete genomes
... Thank you for your reply! I have considered getting representatives for broad classes. My plan was to use CD-HIT to remove redundancy once I had downloaded all of the bacterial and fungal complete genomes, do you think this is the best method? I have used Kraken2 but I want to access the bam fil ...
written 13 months ago by c.e.chong20
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Bowtie database of all bacterial and fungal complete genomes
... Hi all, I would like to create a database of all the bacterial and fungal complete genomes in the RefSeq database to map all of my Metagenome samples to it. Does anyone know if this is possible? The manual states that you have to input a comma separated list of fasta files to build the database, ...
bowtie2 metagenomics mapping shotgun written 13 months ago by c.e.chong20

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Popular Question 12 months ago, created a question with more than 1,000 views. For bbmap split paired-end reads back into separated fastq files?
Popular Question 13 months ago, created a question with more than 1,000 views. For bbmap split paired-end reads back into separated fastq files?

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