User: mastal511

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mastal5111.7k
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Posts by mastal511

<prev • 244 results • page 1 of 25 • next >
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Comment: C: Visualising indexed and sorted bam files
... You can use the Broad Institute's IGV to look at the data. ...
written 16 days ago by mastal5111.7k
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Comment: C: DeSeq2 MA plot
... What version of DESeq 2 are you using? Note that the MA plots shown in the current DESeq2 vignette plot res or resLFC, and you are plotting dds. Link to DESeq2 vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html ...
written 11 weeks ago by mastal5111.7k
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Comment: C: How to find and download the Database from a particular gene in NCBI
... Sounds like the OP is maybe referring to metagenomics? ...
written 3 months ago by mastal5111.7k
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Answer: A: Compare pairs of key/value of perl hash tables
... You could iterate through one hash, and for each gene ID (location) key in the hash, check if it is present in the other hash, and whether the values are the same, and print out the Location and Position when you find matching values. But you would have to make hashes of arrays, because hash keys i ...
written 3 months ago by mastal5111.7k
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Answer: A: FastQC and adapters
... If you are referring to the FastQC per base sequence content plots, it depends on what type of data you have. For RNA-Seq data the pattern you see for the first n bases is thought to be due to the random-priming not being quite so random. I think also for Nextera data, the transposase may be biased ...
written 3 months ago by mastal5111.7k
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Answer: C: Read length difference between the analysis type and true reads
... The explanation for having one base more than expected (e.g. 101 instead of 100), is that for Illumina data, the phasing for each position in the read depends also on the data from the next base, so the last base in the read will always have a much worse base quality, because there is no data from a ...
written 3 months ago by mastal5111.7k
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Comment: C: duplicate read names in TCGA raw bam file
... I've had the opposite problem (bedtools bamtofastq did not give the required results, Picard tools did the job), but with single end data, so I don't know what would happen for paired-end reads. The bam files had multiple entries for some of the reads, which were multi-mappers. With bedtools bamtof ...
written 3 months ago by mastal5111.7k
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Answer: A: Explanation of ENSEMBL GTF features
... UTR stands for UnTranslated Region, so the UTRs should be included in both the gene and transcript. Introns should not be included in the transcript. Check the coordinates for a few of the genes annotated in the gtf file. ...
written 3 months ago by mastal5111.7k
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Comment: C: Quick question about analysis of log2 RMA data
... Yes, you're right, you get a log2FoldChange rather than a Fold-Change. 0.5 is not double the intensity of 0.25 because those were the log2 values of the intensities. ...
written 3 months ago by mastal5111.7k
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Comment: C: Quick question about analysis of log2 RMA data
... If your values are already log2 of the intensities, then you get the difference by subtracting the log2 values, because log(A/B) = log(A) - log(B). This is equivalent to dividing the initial (base 10) intensities, A/B, so essentially it gives you a fold-change. ...
written 3 months ago by mastal5111.7k

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