User: goodez

gravatar for goodez
goodez460
Reputation:
460
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Trusted
Location:
United States
Last seen:
4 days, 20 hours ago
Joined:
9 months, 2 weeks ago
Email:
z*********@gmail.com

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

Posts by goodez

<prev • 131 results • page 1 of 14 • next >
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Comment: C: for low coverage RNAseq how many reads assigned is the bare minimum for differen
... Depends on the genome. For example, you need more read depth for human alignments than you do for fly alignments. > What is the bare minimum number of reads I can use for differential > gene expression analysis? There's not really a bare minimum. Depends how sensitive your analysis is. Also ...
written 5 days ago by goodez460
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Comment: C: Explanation? Read depth, quality, and assembly accuracy in Methylome analysis co
... It's hard to say much without seeing the data, but it's probably fine. I recommend FastQC to check quality of the raw data. Sorry that I can't help much with methylation analysis. I'm not familiar with that. ...
written 12 days ago by goodez460
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Comment: C: Explanation? Read depth, quality, and assembly accuracy in Methylome analysis co
... Just one thing I'd point out is the difference between sequencing quality and mapping quality. Both have scores associated with them, but they mean different things. Sequencing quality is based on the confidence of correctly calling a given nucleotide. Mapping quality refers to the confidence of the ...
written 12 days ago by goodez460
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Answer: A: Obtain Number of PE Reads in BAM file Mapped to Each Chromosome
... 1) Number of properly paired, mapped reads only on chr1: samtools view -f 1 -F 12 -b file.bam chr1 | wc -l 2) It's possible for only first pair to be unmapped, or only second pair, so combine two commands: samtools view -f 4 -F 264 file.bam chr1 | wc -l samtools view -f 8 - ...
written 16 days ago by goodez460
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Comment: C: Where to find a list of stress response genes?
... And more on the warnings as a bioinformatician: I'm happy with all the advice and I totally agree, but I think we just want to see generally if the effect goes away after excluding a set of stress genes. Fixing the problem at the wet-lab stage is definitely the best solution. ...
written 8 weeks ago by goodez460
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Comment: C: Where to find a list of stress response genes?
... Can you explain the final part? `!seen[$1]++`. I enjoy solving problems with awk, but I'm a novice at best. Also out of curiosity, could I replace this: awk 'BEGIN {FS="\t"}; $3 == "gene"; {print $9}' Homo_sapiens.GRCh38.78.gtf with: awk `$3 == "gene"` Homo_sapiens.GRCh38.78.gtf | cut -f ...
written 8 weeks ago by goodez460
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Comment: C: How to read this type of data in R?
... OPs got their priorities straight. Quick access to League of Legends, Discord, and Steam. Are you doing homework? ...
written 9 weeks ago by goodez460
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Comment: C: Meaning of the 5th column in repeatmasker BED format results
... Column 5 is an optional field for BED files. The description of field 5 is below, from [UCSC][1] > **5. Score** - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value > will determine the level of gray in which this feature ...
written 9 weeks ago by goodez460
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Comment: C: Pindel -x option
... Or just filter the results after running pindel. ...
written 9 weeks ago by goodez460
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Comment: C: Issues with Marking Duplicates in Picard
... Sorry to hear that. I personally have had issues every time I've tried to use any Picard tool... Do you require duplicate removal in your analysis? Removing duplicates is often unnecessary and can even falsely remove unique reads. ...
written 10 weeks ago by goodez460

Latest awards to goodez

Scholar 10 weeks ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Appreciated 3 months ago, created a post with more than 5 votes. For C: SNPGenie: CDS does not have length that is divisible by 3
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question
Centurion 3 months ago, created 100 posts.
Scholar 4 months ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Meaning of Decimal points in ENST notation
Scholar 7 months ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Rising Star 7 months ago, created 50 posts within first three months of joining.
Autobiographer 7 months ago, has more than 80 characters in the information field of the user's profile.
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question

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