Useful commands:
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Generate fasta lentgh:
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Linear Fasta:
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or
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Split GAG tbl for each Contig (useful for tbl2asn)
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Calculate average from a column (e.g. 2nd column)
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Download paired fastq files from a SRA/ENA accession list
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Sort longest best hits BLAST tab format (m8 or outfmt6)
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Get a subset from a fasta/q file (e.g. 10%)
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Convert blast tabular output (m8 or outfmt 6) to bed
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Remove/delete sequences by ID from multifasta
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Count base frequency each sequence in multifasta file.
(X is to count the number of masked sites made by bedtools maskfasta -mc X) |
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Convert Blast Results To Gff
(using bp_search2gff.pl) |
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Calculate average per gene in a bed file (example with GeneID at column 4 and values to be averaged in column 2 and 3)
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