User: tw617

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tw61730
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5 months ago
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Posts by tw617

<prev • 16 results • page 1 of 2 • next >
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Comment: C: How to find a variant in a particular position in a bam file only using samtools
... **THANK YOU!** $ samtools mpileup -v -u out.bam | grep "17375390" | cut -f 8 > out.vcf Now I just need to learn how to interpret a vcf file! ...
written 5 months ago by tw61730
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Comment: C: How to find a variant in a particular position in a bam file only using samtools
... Thanks for the reply but I can already see it in IGV, I need to be able to show it is there using only the bam file. I think I might need to use a particular flag on my bed file modified bam but I am having trouble figuring out which one I need or if I need them at all. ...
written 5 months ago by tw61730
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How to find a variant in a particular position in a bam file only using samtools
... I am trying to find a way to display the presence of a single mismatch at position chr7:17375390 on the reverse strand of an overlapping read in a bam file using only samtools. I sliced the section of the chromosome, and I can see that there is a C aligning to T in the reference at this position in ...
bam samtools sam written 5 months ago by tw61730 • updated 5 months ago by swbarnes26.2k
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Answer: A: model design in rna seq - deseq2
... Your method of adjusting the p-value could be too stringent. Look into the default settings of DEseq and see which method is used. We should assume there are many false positives by the nature of the test, 20 DE genes is way too low. You should check the quality of your data while you are at it too, ...
written 5 months ago by tw61730
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Comment: C: IGV genome browser not displaying visualization when BAM file is uploaded
... Ah.... I've figured it out. Thank you for pointing me in the right direction. I only downloaded reads on chromosome 3. ...
written 5 months ago by tw61730
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Comment: C: IGV genome browser not displaying visualization when BAM file is uploaded
... Yes, I tried zooming in and there is nothing there. ...
written 5 months ago by tw61730
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IGV genome browser not displaying visualization when BAM file is uploaded
... Hi, I have a BAM file that I am trying to visualize against the hg19 genome in IGV. I created an index for the file and hg19 is loaded in IGV. When I drag and drop the file there is nothing displayed. It seems like I may have to create an alias file, but the chromosome names in the bam file seem lik ...
alignment igv written 5 months ago by tw61730 • updated 5 months ago by genomax70k
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Answer: A: What are the available automated microscopy options in 2018?
... I am a cytotechnologist that is studying bioinformatics so I am very interested in doing something similar to you in the future... but with cytology specimens. I think "Whole Slide Imaging Tech" is what you are looking for. It is very time consuming, data intensive, and EXPENSIVE. I work in an acad ...
written 8 months ago by tw61730
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Easiest way to Get gene Id's from Affymetrix Probeset id's
... I just did a differential expression analysis of some old microarray data and am looking for a faster way to match gene ids to probeset ids. I used the limma+ebayes method and really only want the gene ids of the TopTable ouput plus a few more. ...
R microarray differential gene expression written 9 months ago by tw61730 • updated 9 months ago by Kevin Blighe47k
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Answer: A: Histogram of p values for all tests
... The two main patterns you should look for when interpreting p-value histograms are: a sharp spike near 0 ( like you have here) that drops off into a somewhat uniform distribution. This indicates that you have some significant differences. The other pattern would be a totally uniform (flat) distribut ...
written 9 months ago by tw61730

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