User: arfesta

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arfesta30
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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 8 months ago by arfesta30
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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 8 months ago by arfesta30
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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 8 months ago by arfesta30
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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 8 months ago by arfesta30 • updated 8 months ago by h.mon15k

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