User: dario.garvan

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dario.garvan450
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Posts by dario.garvan

<prev • 65 results • page 1 of 7 • next >
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Answer: A: how to deal with batch effect in TCGA RNA-seq dataset
... TCGA doesn't provide much useful information for doing quality control. You won't be able to input known batches. Another good approach is to use housekeeping genes as controls that should be made more similar between samples. [RUVSeq][1] has functions for estimating batch effects with such genes or ...
written 12 weeks ago by dario.garvan450
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Comment: C: Clumpify Input via Process Substitution
... Yes, because I made a reduced example which has 1000 reads in each file to test out different approaches. I am using 512 GB RAM and multiple threads on actual data. ...
written 3 months ago by dario.garvan450
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Answer: A: Clumpify Input via Process Substitution
... If there's a lot of extra space on the computer's scratch directory, the easiest to read code would be. cat ${R1[@]} > /scratch/projectID/Patient1_merged_R1.fastq.gz cat ${R2[@]} > /scratch/projectID/Patient1_merged_R2.fastq.gz clumpify.sh -Xmx1g t=1 in1=/scratch/projectID/Patient ...
written 3 months ago by dario.garvan450
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Comment: C: Clumpify Input via Process Substitution
... It's a good answer, but adds an additional software to the pipeline, increasing the future maintenance. ...
written 3 months ago by dario.garvan450
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Comment: C: Clumpify Input via Process Substitution
... I've chosen this as the best answer because it doesn't create extra dependencies. ...
written 3 months ago by dario.garvan450
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Comment: C: Clumpify Input via Process Substitution
... After your suggestion, I did. However, the error remains the same. ``` $ java -ea -cp /usr/local/bbmap/37.98/current/ clump.Clumpify in1=<(cat ${R1[@]}) in2=<(cat ${R2[@]}) out1=$R1output out2=$R2output dedupe subs=1 ``` again produces ``` Starting cris 0. Exception in thread "main" java.la ...
written 3 months ago by dario.garvan450
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7 follow
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Clumpify Input via Process Substitution
... How can I input reads from a file descriptor rather than an actual text file? I have created four small test FASTQ files to identify the problem; two R1 files and two R2 files. If I use process substitution, Clumpify fails. If I firstly combine R1 reads into a text file on disk and R2 reads into ano ...
clumpify bbmap written 3 months ago by dario.garvan450
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Comment: C: Efficent Estimation of Sequencing Coverage
... The percentage of reads aligned isn't output by `bwa mem` at the end of alignment process, unlike Bowtie 2, unfortunately. ...
written 4 months ago by dario.garvan450
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Efficent Estimation of Sequencing Coverage
... I am using [MELT][1], a tool which annoyingly requires the user to specify the [coverage of each BAM file as an input parameter][2]. > Please use a tool to determine approximate (+/- 2x) coverage prior to analysis. The data I have is whole genome sequencing data of 55 humans, which, based on f ...
samtools coverage written 4 months ago by dario.garvan450 • updated 4 months ago by harold.smith.tarheel4.4k
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Answer: A: Using expression array data to predict ethnicty
... It is possible. Any multi-class classification algorithm would be applicable, such as multinomial logistic regression or random forest. ...
written 16 months ago by dario.garvan450

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Supporter 3 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For A: Pretty display of values for samples arranged in a 384-well plate (in R).
Popular Question 16 months ago, created a question with more than 1,000 views. For Unusual Cox Proportional Hazards Results for Highly Expressed Microarray Probes
Scholar 16 months ago, created an answer that has been accepted. For A: Pretty display of values for samples arranged in a 384-well plate (in R).
Scholar 2.3 years ago, created an answer that has been accepted. For A: Pretty display of values for samples arranged in a 384-well plate (in R).
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Large Tables In Supplementary Pdf In Journal Articles
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Fixing Encode Rna-Seq Fastq Files
Scholar 3.2 years ago, created an answer that has been accepted. For A: Pretty display of values for samples arranged in a 384-well plate (in R).
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: RNA-seq replicates pooled before sequencing. How to proceed with DGE analysis?
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Count 5'End Mapped To A Specific Genomic Position
Appreciated 4.8 years ago, created a post with more than 5 votes. For Large Tables In Supplementary Pdf In Journal Articles
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Popular Question 5.2 years ago, created a question with more than 1,000 views. For Large Tables In Supplementary Pdf In Journal Articles
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Count 5'End Mapped To A Specific Genomic Position

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