User: goodez

gravatar for goodez
goodez280
Reputation:
280
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Trusted
Location:
KCMO, United States
Last seen:
1 day, 21 hours ago
Joined:
5 months, 2 weeks ago
Email:
z*********@gmail.com

M.S. in Bioinformatics and Genomics. Always looking to expand my programming experience.

Posts by goodez

<prev • 93 results • page 1 of 10 • next >
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Answer: A: make a reference genome for BRIG (pan-genome analysis)
... The reference genome will be in fasta format right? You can simply `cat genome1.fa genome2.fa genome3.fa . . . > genomes.fa` One caveat is that each fasta header needs a unique name. For example, there may be `chr1` in multiple genomes. So you may need to make them unique, such as: `chr1_genome1 ...
written 2 days ago by goodez280
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Comment: C: Can one use STAR (splice-aware) to align genomic DNA (non-spliced)
... Thank you. I'm assuming you mean check if I have spliced alignments? Because my reads are most definitely not spliced. I actually started a bowtie2 alignment. So I guess I can compare the STAR and bowtie2 results and report back later. ...
written 2 days ago by goodez280
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Comment: C: Can one use STAR (splice-aware) to align genomic DNA (non-spliced)
... What do you mean I shouldn't get spliced reads? I already have the reads, which come from DNA sequence so nothing is spliced. I really need to know how STAR handles aligning unspliced DNA sequence across an exon junction. Since, of course, STAR is expecting reads to be spliced, but will it still cor ...
written 2 days ago by goodez280
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Can one use STAR (splice-aware) to align genomic DNA (non-spliced)
... I have aligned GRO-seq (think ChIP-seq) reads using STAR in splice-aware mode. Will my reads still align correctly if they cross an exon-intron boundary. I would think they should. This may seem like a strange question and perhaps I should have used bowtie2 or something splice-unaware. But I know ST ...
genome chip-seq written 2 days ago by goodez280
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Comment: C: GFF file multiple features for 1 gene region, how to collapse into 1?
... Hi Noob, Your file somewhat resembles a BED, but it's quite confusing. Anyway, start with this to filter for only gene features: ``` awk '$8 == "gene"' your_file.bed > your_file.genes.bed ``` Now you should only have genes, which may still overlap, but will be unique genes. ...
written 3 days ago by goodez280
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Comment: C: How I can pars this file by R or bash?
... That is not how awk works. At least make an attempt to read some documentation ...
written 4 days ago by goodez280
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How/where to obtain a bigwig or bedgraph of unmappable genome regions?
... I want to keep it simple. I need a track file (bigwig or bedgraph) for **hg38** that only contains unmappable regions. It should look like this: chr2 2999982 3000001 1 chr2 3000272 3000275 1 chr2 3000286 3000307 1 chr2 3000453 3000457 1 chr2 3000482 3000488 1 chr2 3000 ...
genome alignment written 6 days ago by goodez280
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Comment: C: DESeq2 DEG analysis using different sequencing depth data
... I use `edgeR` rather than `DESeq2`, but I know they are pretty similar. `edgeR` will normalize for sequencing depth (using TMM method by default). I'm sure `DESeq2` also uses a similar step during a standard workflow. Does `DESeq2` use raw read counts, or something like RPKM? `edgeR` uses raw counts ...
written 6 days ago by goodez280
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Answer: A: Where to find snRNA annotations?
... I think I have found a solution, but I'm curious if anyone else would approach this differently? I obtained a GTF file for hg38, and then used `grep` to find snRNA genes: $ awk '$3=="gene"' hg38.Ens_91.gtf | grep "snRNA" | cut -f9 | cut -c10-24 > snRNA_IDs.txt $ head snRNA_IDs.tx ...
written 13 days ago by goodez280
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Where to find snRNA annotations?
... I am working with some ChIP-seq data and I need to evaluate coverage of snRNA genes. Currently I have a BED file of all noncoding-RNA genes. Where can I find a list of snRNA genes to use as a filter for my noncoding-RNA genes? Or does there already exist somewhere an annotation file of just snRNAs? ...
annotation chip-seq written 13 days ago by goodez280

Latest awards to goodez

Scholar 13 days ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Meaning of Decimal points in ENST notation
Scholar 3 months ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Rising Star 3 months ago, created 50 posts within first three months of joining.
Autobiographer 3 months ago, has more than 80 characters in the information field of the user's profile.
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question

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