User: DNAngel

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DNAngel120
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Posts by DNAngel

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Comment: C: How do you download the nt database for Kraken2?
... Right, and then if I wanted to make my own custom database with my own sequences I would just download them manually and add it to my $DBname. I'd use kraken2-build --add-to-library my_seqs.fasta --db $DBname where $DBname would be what I used earlier for nt database ...
written 15 days ago by DNAngel120
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Comment: C: How do you download the nt database for Kraken2?
... Ohhh I think the download_taxonomy.sh script already includes by default a link to the NCBI nt database, is this correct? Derp... ...
written 15 days ago by DNAngel120
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Comment: C: How do you download the nt database for Kraken2?
... I am still lost as to how to direct my kraken2 commands to the nt database. I get that $DBname now is just a name I choose to call my database, but how am I telling kraken2 to build me my database using nt as the source? Should I download the nt database somewhere in my folder and refer to it? Then ...
written 15 days ago by DNAngel120
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Comment: C: How do you download the nt database for Kraken2?
... Sorry had to go MIA for a while due to family. I am back at it with trying out kraken2. I still don't understand where I'm supposed to direct kraken2-build for the nt database. I understand hat $DBname is just the name I choose, but how do I direct it to download taxonomy from the nt database? ...
written 15 days ago by DNAngel120
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Comment: C: What to do with mapped reads after assembly?
... Doing an actual assembly would mean de novo right? So without a reference genome? I also do have a a transcript.fasta.gz file, along with a annotation.gff.gz, a RepeatMasked.gff.gz file and a Repeat.fasta.gz (genome file). The data was given to me to work on although I will specifically be working o ...
written 26 days ago by DNAngel120
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What to do with mapped reads after assembly?
... Hello everyone, Sorry for posting a simple question but although I have worked with some assembly before, I never worked with data at the whole genome scale and I would like to ask for some advice. I followed this tutorial on biostairs: https://www.biostars.org/p/75489/ but I ended up just conver ...
assembly annotation written 27 days ago by DNAngel120
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Comment: C: Error when trying to convert BAM file to FASTQ.
... My new question got removed because they said it was too similar to this. So I just reposted it here. ...
written 4 weeks ago by DNAngel120
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Comment: C: Samtools SORT or bedtools bamToFastq giving error when converting reads to fastq
... Hey, so I just used samtools fastq cert1_unmapped_sorted.bam > cert1_unmapped.fastq and that seemed to work. Same when I used my mapped reads. However I still have to go through the files and check. Is there any particular reason some protocols suggest separating paired end reads into R1 and R2 f ...
written 4 weeks ago by DNAngel120
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Comment: C: Samtools SORT or bedtools bamToFastq giving error when converting reads to fastq
... using samtools flagstat, R1 and R2 are the same number. But if I use bamtools stats, they are slightly off. Not sure why that is... ...
written 4 weeks ago by DNAngel120
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Comment: C: Samtools SORT or bedtools bamToFastq giving error when converting reads to fastq
... Anyways I just added my whole question/pipeline in the original question but I doubt people will realize I have a new question in that post. ...
written 4 weeks ago by DNAngel120

Latest awards to DNAngel

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Scholar 2.2 years ago, created an answer that has been accepted. For A: How to save trimmomatic terminal summary to an output file?

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