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User: Simply Bioinformatics

gravatar for Simply Bioinformatics
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There is no knowledge that is not power

Posts by Simply Bioinformatics

<prev • 19 results • page 1 of 2 • next >
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Answer: A: Overlapping regions in a BedGraph file
... This solution only works for non-Bookended bedgraph file Sort and then merge overlapping regions(mean of score or max, sum, etc) LC_COLLATE=C sort -k1,1 -k2,2n -k3,3n -s in.bdg > out.bdg.tmp bedtools merge -i out.bdg.tmp -c 4 -d 0 -o max > out.bdg LC_COLLATE=C sort -k1,1 -k2,2n -k ...
written 15 months ago by Simply Bioinformatics • 170
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Answer: A: How To Filter Mapped Reads With Samtools
... PROCESSORS=10 **Single_End_Layout:** samtools view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4 in.bam > unmapped.bam **Paired_End_Layout** samtools view --threads $PROCESSORS -b -f 2 in.bam > mapped.bam samtools view ...
written 2.2 years ago by Simply Bioinformatics • 170 • updated 11 months ago by RamRS ♦ 30k
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Answer: A: Expected error filtering on Ion Torrent data using fastq_filter USEARCH command
... **USEARCH Fastq-Filter for Ion-Torrent 16S** usearch -fastq_filter in.fastq -fastqout out.fastq -fastq_ascii 33 -fastq_qmin 0 -fastq_qmax 47 ...
written 2.3 years ago by Simply Bioinformatics • 170
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Answer: A: How can I save the output from samtools and awk as a bam file?
... samtools view --threads 2 -h in.bam | awk '{if($3 != "chrM" && $3 != "chrUn"){print $0}}' | samtools view --threads 2 -Shb - > out.bam ...
written 2.4 years ago by Simply Bioinformatics • 170 • updated 2.4 years ago by genomax ♦ 89k
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Answer: A: bam file flags- interpretation
... Four Main reference Sites that You might need during your adventure: ENJOY ;) 1) https://broadinstitute.github.io/picard/explain-flags.html 2)http://www.samformat.info/sam-format-flag 3)http://www.samformat.info/sam-format-flag-single 4)https://ppotato.wordpress.com/2010/08/25/samtool-bitwise-f ...
written 2.9 years ago by Simply Bioinformatics • 170
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Answer: A: Web Page Converting Seq Mapping Score
... Four Main reference Site that You might need during your adventure: ENJOY ;) 1) https://broadinstitute.github.io/picard/explain-flags.html 2)http://www.samformat.info/sam-format-flag 3)http://www.samformat.info/sam-format-flag-single 4)https://ppotato.wordpress.com/2010/08/25/samtool-bitwise-fl ...
written 2.9 years ago by Simply Bioinformatics • 170
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Answer: A: How to create *.dist file?
... This method will calculate the distance matrix without considering Terminal Gap Penalty dist.seqs(fasta=input.fasta, countends=F) Alternative method is To trim your fasta reads to the most common length 1) trim.seqs(fasta=input.fasta, minlength=300, maxlength=300) 2) dist.seqs(fasta=input.trim. ...
written 2.9 years ago by Simply Bioinformatics • 170
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Answer: A: ChIP-Seq TSS Line Plot
... Have You tried DeepTools? http://deeptools.readthedocs.io/en/latest/content/example_usage.html ![enter image description here][1] [1]: http://deeptools.readthedocs.io/en/latest/_images/start_workflow.png ...
written 2.9 years ago by Simply Bioinformatics • 170
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Answer: A: Plotting TSS & TTS for Chip-seq peaks
... DeepTools http://deeptools.readthedocs.io/en/latest/content/example_usage.html ![][1] [1]: http://deeptools.readthedocs.io/en/latest/_images/start_workflow.png ...
written 2.9 years ago by Simply Bioinformatics • 170
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Answer: A: ENCODE ATAC-seq pipeline peak calling
... This pipeline is currently deprecated and been replaced by this one: https://github.com/kundajelab/atac_dnase_pipelines ...
written 2.9 years ago by Simply Bioinformatics • 170

Latest awards to Simply Bioinformatics

Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Plotting TSS & TTS for Chip-seq peaks
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Plotting TSS & TTS for Chip-seq peaks
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