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Don
I modified a bit your script to output the total count and give some format:

awk -v gene="gene-a gene-b" -v lengths="3 6" -v strings="GCATGAAAACATACA TTTCCAGAAATTGT" '
BEGIN { nString =...

Don
Thanks!
PS. If I would like to search for more than one string (GCATGAAAACATACA and TTTCCAGAAATTGT) and report different number characters (3 and 6. I should be able to do it passing the...

I do have access to awk. I would be interested on seeing a solution with awk too.

I have this fastq file:

@M04961:22:000000000-B5VGJ:1:1101:9280:7106 1:N:0:86
GGGGGGGGGGGGCATGAAAACATACAAACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGAAAAATATCAACCACACCA
+test-1...

I have a file with 48 rows. I am counting 6 rows and adding 6 to that number and repeating the operation, and then output the value in column 1. For the second column, I would like to get sort of a...

I need to cat two files with similar names. I am using the following script:

#!/bin/bash
if [[ -f $1 ]]
then
file=$1
file2="${file%R1.fastq}R2.fastq"
echo fetching...

Guys
Thank you so very much! Bakunin, it did not even cross my mind to use the Hold, Get and Exchange commands for this task. Thanks a TON for a very detailed explanation. Don, thank you so very...

I have this file:

>ID1
AA
>ID2
TTTTTT
>ID-3
AAAAAAAAA
>ID4
TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC

Add I am trying to use this script to output sequences longer than 15 characters:
...

Rudy
Thanks a TON! Quick question, why BEGIN{ RS="^@"; FS="\n" } would not work?

I have this file:

@Muestra-1
agctgcgagctgcgacccgggttatataggaagagacacacacaccccc
+
!@$#%^&*()@^#&HH!&*(@&#*(FT^%$&*()*&^%@
@Muestra-2
agctgcgagctgcgacccgggttatataggaagagacacacacaccccc
+...

Scrutinizer
Your first did the trick
Thanks!

got it ! Thanks

I have a file that look like this:

>Muestra-1
agctgcgagctgcgaccc
gggttatata
ggaagagacacacacaccccc
>Muestra-2
agctgcg
agctgcgacccgggttatataggaagagac
acacacaccccc
>Muestra-3...

That worked like a charm! Thanks a TON!
PS. Still, I am bit curious, would it be possible to fix the script in such way that can be run directly from the cmd terminal?

I have this script (thanks Don!) that runs as expected in cygwin:

gawk -F, 'NR == 1{print "Source,Well_Source,Volume,Destination_Well,Destination"; OFS = ","; next}/Ladder/{next}LAST2 && $2 !=...

I was just flirting with the idea of installing one package (bcl2fas2) on my WSL:Ubuntu using alien. However, when I run

sudo alien bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm

I get the following...

That was the problem actually.
Thanks!

sorry! My bad, I meant :

sed '1isometext' infile


Or even


echo a | sed '1isometext'


return the same error on MAC:


sed: 1: "1isometext": command i expects \ followed by text
...

Super basic question. I installed sed GNU on a MAC running High Sierra. However, when I run sed '1i>sometext, I get the following error:

sed: 1: "1isometext"; command i expects \ followed by...

Rudy
Thanks!

No complains here! Works like a charm!

For my own education, why this wouldnt work?

sed 'N; s/^.*\n//;=;/^[0-9]\+/ s/^/>seq /' file

Or this:

sed '/^>/s/.*//;/^$/=;/^$/d;s/[1-9].*/echo...

I have a fasta file like this one:

>ID1
AAAAAA
>ID2
TTTTTT

And I am using this sed script to increase the count sequence

sed '/^>/s/.*//;/^$/=;/^$/d' text.txt | sed 's/[1-9].*/echo ">seq"...

Thanks a TON! That worked like a charm

This did not work:

sed ':a /^>/!N;s/\r\n?\n\([^>]\)/\1/;ta'

Or this:

sed ':a /^>/!N;s/\r?\n\([^>]\)/\1/;ta'

I am using the following sed script to remove new lines (\r\n and \n), except from lines starting with >:

sed -i ':a /^>/!N;s/\r\n\([^>]\)/\1/;s/\n\([^>]\)/\1/;ta'

Is there a way to include...