User: O.rka

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O.rka230
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Posts by O.rka

<prev • 227 results • page 1 of 23 • next >
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Why are there soo many hits when using KOFAMSCAN?
... Has anyone tried using KOFAMSCAN? I feel like the data is useless unless I'm not using it correctly. There are literally SO many KOFAM hits per gene. What are your thoughts on this? Is it because I'm using it on a metagenomics dataset? It doesn't make sense that almost ever gene has so many hit ...
annotation metagenomics protein written 4 days ago by O.rka230 • updated 4 days ago by Mensur Dlakic8.1k
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Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
... **Why isn't it just the R^2 value and instead multiplying -sign(slope) * R^2 ?** **What does a negative scalefree topology in this event mean?** I'm following the tutorial here: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-man.p ...
wgcna gene expression coexpression written 4 days ago by O.rka230
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Comment: C: WGCNA soft-threshold power selection
... Why are you using `-sign(sft$fitIndices[,3])*sft$fitIndices[,2],` here? ...
written 6 days ago by O.rka230
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How to fix minimap2 -> samtools sort error (samtools sort: truncated file. Aborting)?
... I'm trying to run the following pipeline: ` [minimap2] -> [samtools sort] && [samtools index]` In particular, here's the command I'm running: ``` ( minimap2 -a -x map-ont -t 4 Genomes/E_crus-galli_v2.0/EC.fasta reads.nanofilt.fastq | samtools sort -T tmp -o sorted.bam && samt ...
alignment written 25 days ago by O.rka230
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Combining prodigal for metagenomics and transdecoder for metatranscriptomics in same dataset?
... I have a dataset with overlapping samples. We did metagenomic sequencing for one (I think this may be a coassembly of multiple samples but I'm not sure) and we also have metatranscriptomics for various samples that are related. I ran metaSPAdes and prodigal for ORF calls using the metagenomic read ...
metatranscriptomics metagenomics orf calling written 6 weeks ago by O.rka230
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Comment: C: How to create vcf file with SNPs bed file and sorted bam file?
... I will try the commend above. The reason I asked about the `--dbsnp` argument is because I don't know what to use for this. Is this an input vcf file (https://gatk.broadinstitute.org/hc/en-us/community/posts/360062537671-GATK-4-1-7-0-does-not-annotate-ID-using-dbSNP-build-153-VCF)? Or is this the ...
written 6 weeks ago by O.rka230
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Comment: C: How to create vcf file with SNPs bed file and sorted bam file?
... I've always heard of GATK but I haven't had the pleasure to try it out yet. I just installed 2 conda environments one with `v3.8-1-0-gf15c1c3ef` and `v4.1.9.0`. I didn't see the `--dbsnp` option in either of them. What is that command? This is very helpful. Do you think you could help me figure ...
written 6 weeks ago by O.rka230
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Comment: C: How to create vcf file with SNPs bed file and sorted bam file?
... A bit. I've only really done it for prokaryotic organisms with `snippy`. Right now I'm trying the following: `source activate vcftools_env && pv 201858321_S1.trimmomatic.GCA_000001405.15_GRCh38_no_alt_analysis_set.sorted.bam | samtools view -h | bcftools mpileup -f ../../db/genomes/human ...
written 6 weeks ago by O.rka230
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How to create vcf file with SNPs bed file and sorted bam file?
... I found this post but I'm still not sure how to do this: https://www.biostars.org/p/392006/ Here's my genome file and index: `../../db/genomes/human/GRCh38.p13/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna` `../../db/genomes/human/GRCh38.p13/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fa ...
genome variant rna-seq written 6 weeks ago by O.rka230 • updated 6 weeks ago by Qiongyi100
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Comment: C: metabat installation problem with conda
... What does this mean? bioconda/label/cf201901 Is it a part of the bioconda channel? I don't get it. ...
written 8 weeks ago by O.rka230

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For Gene ontology-type analysis but with protein domain IDs? (e.g. TIGRFAM, PFAM)
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Gene ontology-type analysis but with protein domain IDs? (e.g. TIGRFAM, PFAM)
Popular Question 5 months ago, created a question with more than 1,000 views. For Gene ontology-type analysis but with protein domain IDs? (e.g. TIGRFAM, PFAM)
Popular Question 5 months ago, created a question with more than 1,000 views. For Where to download gff3 file for EcoCyc data?
Popular Question 5 months ago, created a question with more than 1,000 views. For Gene ontology-type analysis but with protein domain IDs? (e.g. TIGRFAM, PFAM)
Popular Question 6 months ago, created a question with more than 1,000 views. For Gene ontology-type analysis but with protein domain IDs? (e.g. TIGRFAM, PFAM)
Popular Question 6 months ago, created a question with more than 1,000 views. For Where to download gff3 file for EcoCyc data?
Great Question 8 months ago, created a question with more than 5,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 8 months ago, created a question with more than 1,000 views. For Gene ontology-type analysis but with protein domain IDs? (e.g. TIGRFAM, PFAM)
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Popular Question 12 months ago, created a question with more than 1,000 views. For How to repair a gff/gtf file that is missing gene id, gene name, and transcript name?
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