User: Simply Bioinformatics

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Posts by Simply Bioinformatics

<prev • 19 results • page 2 of 2 • next >
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Answer: A: ATAC-seq peak calling with MACS
... We Are Using This: macs2 callpeak -t input -f BED -g "hs" -p 0.01 --nomodel --shift -37 --extsize 73 -B --SPMR --keep-dup all --call-summits Currently, there is an existing issue on MACS2 which intermittent -1 as pValue which will crash the IDR as downstream analysis as a heads up: convert all - ...
written 2.9 years ago by Simply Bioinformatics170
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Answer: A: Number Of Reads In A Sam File Which Are Assigned To Each Chromosome?
... This is the Samtools Solution + bash Enjoy PROCESSORS=10 BAM=blah.bam | blah.sam samtools view --threads $PROCESSORS $BAM | cut -f 3 | sort | uniq -c | sort -nr | sed -e 's/^ *//;s/ /\t/' | awk 'OFS="\t" {print $2,$1}' | sort -n -k1,1 > Chr_freqs.txt ...
written 3.0 years ago by Simply Bioinformatics170 • updated 12 months ago by RamRS30k
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Answer: A: Extraction of first sequences from a big fasta file
... REQUESTED_LINES=10 awk "/^>/ {n++} n>$REQUESTED_LINES {exit} {print}" input.fasta > output.fasta ...
written 3.0 years ago by Simply Bioinformatics170 • updated 16 months ago by RamRS30k
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Answer: A: Remove mitochondrial reads from BAM files
... This solution will keep the headers intact so you can extract fastq file samtools view -h this.bam | awk '{if($3 != "chrM" && $3 != "chrUn"){print $0}}' | samtools view -Shb - > this.filter.bam ...
written 3.0 years ago by Simply Bioinformatics170
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Answer: A: Tools For Metagenomic Data Analysis
... 16S Metagenomics: Mothur: https://www.mothur.org/wiki/Category:Commands Usearch: http://www.drive5.com/usearch/manual/ Qiime: http://qiime.org/scripts/ ...
written 3.1 years ago by Simply Bioinformatics170
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Answer: A: problems on hierarchical clustering
... The only way to get rid of this bug is to downgrade your R version to 3.0.2. ¯\\_(ツ)_/¯ or user R-Switch: https://r.research.att.com/#other ...
written 3.3 years ago by Simply Bioinformatics170
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Answer: A: How To Solve An Out-Of-Memory Error When Using Usearch Chimera Detection
... Just split you file into separate chunk and run uchime_ref in for loop ...
written 4.1 years ago by Simply Bioinformatics170
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Answer: A: Tools For Metagenomic Data Analysis
... Hi,  I recently find these two software pretty useful : Gene Calling: prodigal  : http://prodigal.ornl.gov/server.html pathway and function prediction: picrust : http://picrust.github.io/picrust/   ...
written 5.6 years ago by Simply Bioinformatics170
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Answer: A: What Is The Best Pipeline For 16S Rna Metagenome Analysis?
... Mothur has one of the best tutorials around, if you are curious about each step of metagenome analysis included brilliant step by step tutorial also  https://www.mothur.org/wiki/MiSeq_SOP https://www.mothur.org/wiki/454_SOP ...
written 5.6 years ago by Simply Bioinformatics170

Latest awards to Simply Bioinformatics

Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Plotting TSS & TTS for Chip-seq peaks
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Plotting TSS & TTS for Chip-seq peaks

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