User: ajajoo

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ajajoo0
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Posts by ajajoo

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bwa mem to feature Counts
... bwa mem -t $Ncpu -k 14 -T 1 -L 3,3 -O 6,6 -E 3,3 ../humangenomes/hg38.fa $filename.R1.fastq.gz $filename.R2.fastq.gz | samtools view -Sbh > $filename.bam Can I use above bam file for feature counts, how will it handle chimeric alignment and what is the quality for linear match with the above ...
featurecounts bwa mem written 6 weeks ago by ajajoo0 • updated 6 weeks ago by swbarnes2330
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Comment: C: DESeq2 for big data sets
... thank you for replying. ...
written 11 weeks ago by ajajoo0
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DESeq2 for big data sets
... I used DESeq2 for around 2500 subjects. I used parallel true option and it used around 40 processors. It took about 1.5 weeks to perform estimating dispersions, fitting model and testing, etc all the way till final dispersion estimates. It also displayed replacing outliers for ** genes etc. But afte ...
deseq2 written 11 weeks ago by ajajoo0 • updated 11 weeks ago by Michael Love26k

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