User: mastal511

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mastal5111.8k
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Posts by mastal511

<prev • 255 results • page 1 of 26 • next >
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Comment: C: Gene pathway analysis of my list of genes
... There are a couple of R packages which work together called Gage and Pathview, they use KEGG pathway information. ...
written 13 days ago by mastal5111.8k
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Answer: A: determine what best alignment tool when using R on fastq files?
... Use alignment tools - there are various aligners - bwa, bowtie, BBMap. ...
written 14 days ago by mastal5111.8k
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Comment: C: How to produce a consensus genome
... Velvet has 2 steps - velveth and velvetg. ...
written 3 months ago by mastal5111.8k
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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 3 months ago by mastal5111.8k
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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 3 months ago by mastal5111.8k
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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 3 months ago by mastal5111.8k
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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 3 months ago by mastal5111.8k
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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 3 months ago by mastal5111.8k
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Comment: C: bowtie -n aligment mode
... the seed length is just a 'seed' or starting point for the alignment. ...
written 4 months ago by mastal5111.8k
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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 5 months ago by mastal5111.8k

Latest awards to mastal511

Scholar 8 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Scholar 9 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Scholar 9 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Learning Biology/Bioinformatic Basics
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Weird fastq format
Scholar 10 months ago, created an answer that has been accepted. For A: Mapping to the transcriptome using Bowtie - am I doing it right?
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