bedtools map : map overlapping features and calculate sum, count, min, max, mean, median

https://bedtools.readthedocs.io/en/latest/content/tools/map.html

bedtools map allows one to map overlapping features in a B file onto features in an A file and apply statistics and/or summary operations on those features.

parallel-fastq-dump

https://github.com/rvalieris/parallel-fastq-dump

parallel fastq-dump wrapper

print range of columns

https://unix.stackexchange.com/questions/532599/awk-print-range-of-columns

input:

column1,column2,column3,column4,column5,column6,column7,column8

output:

column2,column3,column4,column5,column6,column7

Answer

cut -d, -f2-7 <input-file>

or

$ awk -v b=2 -v e=7 'BEGIN{FS=OFS=","} {for (i=b;i<=e;i++) printf "%s%s", $i, (i<e ? OFS : ORS)}' file

b=beginning field number, e=end field number.

Adding a Column of values in a tab delimited file

https://unix.stackexchange.com/questions/117568/adding-a-column-of-values-in-a-tab-delimited-file

Input file:

SPATA17 1   217947738
LYPLAL1 1   219383905
FAM47E  4   77192838
SHROOM3 4   77660162
SHROOM3 4   77660731
SHROOM3 4   77662248

Output file:

SPATA17 1   217947738 file1
LYPLAL1 1   219383905 file1
FAM47E  4   77192838  file1
SHROOM3 4   77660162  file1
SHROOM3 4   77660731  file1
SHROOM3 4   77662248  file1

Answer

for file in *; do awk 'BEGIN{OFS="\t"}{print $0, FILENAME}' $file; done

FILENAME is a variable in awk, it expand to current file name that awk is processing.

How to replace dot in linux

https://stackoverflow.com/questions/27205566/how-to-replace-dot-in-linux

# substitute . to NA

awk 'BEGIN {OFS=FS="\t"} {for (i=1;i<=NF;i++) {gsub(/^\.$/,"NA",$i)}}1' file

/^\.$/ to assure that nothing precedes or follows the dot

Tophat2 vs HISAT vs STAR

Tophat2 is not bad 
http://cdwscience.blogspot.com/2019/01/tophat-really-isnt-that-bad.html
 
https://genomespot.blogspot.com/2015/03/hisat-vs-star-vs-tophat2-vs-olego-vs.html



Tophat2 is bad
Question: HISAT2 or Tophat2
https://www.biostars.org/p/230724/

bedops --chop : chop bed into identical intervals

https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html

The --chop operator merges all overlapping input regions and “chops” them up into a set of disjoint segments of identical length (with a default of one base). One or more input files may be provided; this option will segment regions from all inputs:

Note

Overlapping and nested regions are merged into contiguous ranges before chopping. The end result contains unique, non-overlapping elements.

(base) [lee@ko44 annotation]$ more chrom.sizes.chr.TAIR10.bed
chr1    0    30427671
chr2    0    19698289 
chr3    0    23459830
chr4    0    18585056
chr5    0    26975502

 (base) [lee@ko44 annotation]$ bedops --chop 1000 chrom.sizes.chr.TAIR10.bed > arabidopsis_1kb_chr1_5.bed

(base) [lee@ko44 annotation]$ more arabidopsis_1kb_chr1_5.bed
chr1    0    1000
chr1    1000    2000
chr1    2000    3000
chr1    3000    4000
chr1    4000    5000
chr1    5000    6000
chr1    6000    7000
chr1    7000    8000