User: O.rka

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O.rka30
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Posts by O.rka

<prev • 24 results • page 1 of 3 • next >
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Set percent identity and percent length covered in HISAT2 mapping
... I am comfortable using [HISAT2](https://ccb.jhu.edu/software/hisat2/manual.shtml) and would like to change the percent identity and length covered in the mapping. An example of these parameters is in CLC mapping tool. **How can I do this in HISAT2?** http://resources.qiagenbioinformatics.com/manu ...
read hisat2 mapping genomics sequencing written 7 days ago by O.rka30
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Comment: C: Efficiently Iterating Over Fastq Records From Python
... Is it faster to write a fastq file record by record or to make a list of records and then write the list of records? ...
written 23 days ago by O.rka30
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How to download all transcripts from Mouse with exons as upper case and introns as lower case?
... I was using UCSC's Table Browser before but you have to input the transcript IDs and most of the time the databases don't match up completely for ensembl and many transcripts are left out of the mix. **Is there a way in Ensembl or something where I can just download all of the sequences where the e ...
genome mouse database sequences rna-seq written 23 days ago by O.rka30
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Functional information from de-novo orf calling in genome bins?
... I have a metagenome that I've binned out into individual genomes. I called all of the ORFs on all of the contigs and they are organized in protein fasta files (*.faa) for each genome bin. **How can I assign functional information to these genome bins?** I'm running [Genome Properties](https:// ...
de-novo orf functional genomics properties written 3 months ago by O.rka30
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Comment: C: binary phenotype or discrete traits in wgcna analysis
... Any luck or progress on this? ...
written 4 months ago by O.rka30
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Answer: A: Biopython hmmscan parser
... This is the one I wrote. I need to do some error handling for when there are no hits b/c it will break. I put stuff like this in my `Jupyter` profile and it speeds stuff up... a lot. def read_hmmscan(path, set_index="query_name", sort_values="sequence|_|e-value"): # Build pd.DataFram ...
written 5 months ago by O.rka30
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Comment: C: any recommended tools for batch effect and normalization not written in R?
... Did you find anything? Also, what is the model matrix in https://github.com/brentp/combat.py? ...
written 5 months ago by O.rka30
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Comment: C: Rpkm Calculation For Genes
... Can somebody confirm that this is the same equation as http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/? Why is 10^9 different that 1e6? CORRECTION: nevermind, I didn't see the 1e3 incorporated in one of the other eqns ...
written 6 months ago by O.rka30
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Advice on assembling very large metagenomic dataset?
... I need to assemble a large metagenomics dataset from [Illumina NextSeq](https://www.illumina.com/systems/sequencing-platforms/nextseq.html) reads. My read depth is approximately 20 million reads per sample (28 samples) and the concatenated R1 and R2 reads are 130 GB each. I'm using 64-threads and i ...
assembly metagenomics big-data genomics large written 6 months ago by O.rka30 • updated 6 months ago by yzzhang30
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Weighted network (WGCNA) and Hive plot. Too many edges?
... I just found out about [Hive plots](http://www.hiveplot.net/) recently. Incredible method for viewing network structure and I am eager to try it out! I've been transitioning to weighted networks from unweighted networks and have been creating weighted networks using WGCNA. In weighted networks, e ...
wgcna network gene-expression rna-seq hive plot written 7 months ago by O.rka30

Latest awards to O.rka

Supporter 5 months ago, voted at least 25 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For How to tell bloodtype from SNPs data?
Student 13 months ago, asked a question with at least 3 up-votes. For Most up-to-date Gene Ontology [GO] analysis?

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