User: goodez

gravatar for goodez
goodez250
Reputation:
250
Status:
Trusted
Location:
KCMO, United States
Last seen:
2 days, 14 hours ago
Joined:
3 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 • 72 results • page 1 of 8 • next >
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Comment: C: How to use edgeR to compare multiple conditions to reference condtiion
... I know this is old, but why isn't it `coef=2:5`?? ...
written 11 days ago by goodez250
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Comment: C: What is a read group?
... Which Picard tools are you trying to use? This [page][1] has some good discussion of read group. [1]: https://gatkforums.broadinstitute.org/gatk/discussion/6472/read-groups ...
written 19 days ago by goodez250
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Comment: C: Quick and easy way to get alignment stats from many SAM/BAM files?
... Thanks -- not sure how I didn't come across this ...
written 4 weeks ago by goodez250
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5 follow
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Quick and easy way to get alignment stats from many SAM/BAM files?
... Is there a good tool for extracting basic alignment stats from multiple BAMs/SAMs? I have tried `CollectAlignmentSummaryMetrics` from Picard and I really don't like it. I just want simple statistics such as: SAMPLE, TOTAL READS, ALIGNED READS, UNIQUELY MAPPED READS It would be best if this we ...
alignment rna-seq written 4 weeks ago by goodez250
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Comment: C: Merging individual .bed files?
... > 2). Is it possible to create an individual .bed file using bamtobed tools for each .bam file and then merge these .bed files? Yes. You can make individual BED files from each BAM. Then merge the BED files using a tool like `bedtools merge` ...
written 5 weeks ago by goodez250
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Comment: C: Difference in BAM coverage between bedtools output and IGV coverage track
... I'm a little confused by your question, but if you are viewing a BAM with IGV, then you are seeing all reads. The BAM file will have all of your reads unless you filtered the BAM file, but I don't think you did. ...
written 5 weeks ago by goodez250
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Comment: C: Question on BIGWIG tracks from Chip Seq experiments
... 1) Link was broken for me 2) The peaks must correspond to a protein binding the DNA at those spots, as detected by a given antibody. Maybe the peaks are at different spots due to different antibodies or different conditions. Need a picture or working link to help any more. ...
written 6 weeks ago by goodez250
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Comment: C: ChIPseq vs RNAseq results comparison
... Would you do any normalization to the ChIP? Or just take raw counts? ...
written 6 weeks ago by goodez250
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Answer: A: Meaning of Decimal points in ENST notation
... [https://www.biostars.org/p/174687/][1] You can pretty much ignore it. This is from the ensembl website: > For example ENSMUSG00000017167.6. From this we can see that it's an Ensembl ID (ENS), from mouse (MUS), it's a gene (G) and it's on its sixth version (.6). [source][2] [1]: https://ww ...
written 6 weeks ago by goodez250
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Answer: A: filter data based on values
... Using R this will only keep rows where all values are greater than or equal to 2. index <- data >= 2 index <- apply(index, 1, all) data <- data[index,] ...
written 6 weeks ago by goodez250

Latest awards to goodez

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Meaning of Decimal points in ENST notation
Scholar 6 weeks ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Rising Star 7 weeks ago, created 50 posts within first three months of joining.
Autobiographer 7 weeks ago, has more than 80 characters in the information field of the user's profile.
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question

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