User: arfesta

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arfesta10
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Posts by arfesta

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Answer: A: fastQC for Oxford Nanopore reads
... Here are a few tools I've used..I think the question comes down to what exactly do you mean by QC (what stats are you trying to find out): [minion_qc][1] [IONiser][2] [Nanoplot..as seen here on biostars][3] [1]: https://github.com/roblanf/minion_qc [2]: http://bioconductor.org/packages/deve ...
written 16 days ago by arfesta10
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Comment: C: Labelling sequences within fasta files according to sample name.
... Are you doing this for the purpose of adding read groups to the samples? ...
written 16 days ago by arfesta10
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Answer: A: loop for samtools to deal with multiple files
... In terminal why not just try: cd /share/gwascotton/GBS_data/pileup_trial/ ls *.bam > ~/Desktop/list.of.bams while read file; do samtools pileup -c -l /share/gwascotton/GBS_data/merged_files.sorted.bam.pileup -f /share/gwascotton/GBS_data/Ghirsutum_458_v1.0.fa /sh ...
written 16 days ago by arfesta10
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Concatenate RNA-seq technical & biological reps or just technical reps before aligning
... Say my goal is to identify SNPs or Differentially expressed transcripts between 3 main groups: 1. High Fat 2. Medium Fat 3. Low Fat For each group I have 3 biological reps (3 distinct progeny from a specific cross) and 2 technical reps of each biological rep. **Example:** High F ...
alignment rna-seq snp sequencing written 16 days ago by arfesta10 • updated 10 days ago by h.mon8.7k

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