User: mastal511

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mastal5111.7k
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Posts by mastal511

<prev • 253 results • page 1 of 26 • next >
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Comment: C: How to produce a consensus genome
... Velvet has 2 steps - velveth and velvetg. ...
written 22 days ago by mastal5111.7k
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Comment: C: How to add column to a file from from another file having one common column but
... Have a look at this tutorial for the join functions: http://stat545.com/bit001_dplyr-cheatsheet.html ...
written 25 days ago by mastal5111.7k
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Comment: C: How to add column to a file from from another file having one common column but
... If you are familiar with R, the table joining functions in the dplyr package may be helpful. ...
written 25 days ago by mastal5111.7k
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Comment: C: How can I combine different Affymetrix platform?
... The 2 arrays form a set. The U133A array contained more well-known genes, and the U133B more probesets based on evidence from ESTs, and each array contained some 22K probesets. Essentially there are 117 samples, presumably each run on both U133A and U133B, and in total, you have intensity measureme ...
written 28 days ago by mastal5111.7k
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Comment: C: How can I combine different Affymetrix platform?
... Have a look at this previous question, https://www.biostars.org/p/160402/, and at the Affymetrix documentation for the arrays. The Affymetrix HG-U133A and HG-U133B arrays were a set, not different platforms, so you might want to check whether samples from each patient were run on both arrays. Se ...
written 28 days ago by mastal5111.7k
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Comment: C: Adapter percentages in the reads
... It depends on the type of experiment you're doing. If you're not looking at something like small RNAs, then it indicates that the average insert length of the fragmented DNA is shorter than the length of the reads. ...
written 4 weeks ago by mastal5111.7k
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Comment: C: bowtie -n aligment mode
... the seed length is just a 'seed' or starting point for the alignment. ...
written 8 weeks ago by mastal5111.7k
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Comment: C: How does regularized log transformed data from DESeq2 relate to read counts?
... It's not the P-values that are on the log2 scale, it's the number of counts. ...
written 10 weeks ago by mastal5111.7k
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Answer: C: Bam file with unmapped reads from another genome than reference
... Map your reads to hg19 first, remove the reads that map, then align the unmapped reads to the viral genome. ...
written 12 weeks ago by mastal5111.7k
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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 4 months ago by mastal5111.7k

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