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Search: Posts Made By: empyrean
7,742
Posted By empyrean
Thank you , Don. This works really well. easy to...
Thank you , Don. This works really well. easy to run and easy to understand as well.

---------- Post updated at 04:17 PM ---------- Previous update was at 04:16 PM ----------

ahamed, thank you...
7,742
Posted By empyrean
Sorry for the confusion. Here are the input files...
Sorry for the confusion. Here are the input files and required output

This is the input file where it contains unique sequences. i have more than million such unique sequences.
Query:
>tag1...
7,742
Posted By empyrean
[Solved] Count and search by sequence in multiple fasta file
Hello,

I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long...
3,245
Posted By empyrean
Process alternate lines in awk/sed/perl
hi..

i have a fasta file with the following format

>sequence1
CCGGTTTTCGATTTGGTTTGACT
>sequence2
AAAGTGCCGCCAGGTTTTGAGTGT
>sequence3
AGTGCCGCAGAGTTTGTAGTGT

Now, i want to read...
8,352
Posted By empyrean
the above command works for any sequence. But i...
the above command works for any sequence. But i have is fastq file, where the format is completely different which is explained here (http://en.wikipedia.org/wiki/FASTQ_format)

I need to check for...
8,352
Posted By empyrean
Extract length wise sequences from fastq file
I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that?
2,657
Posted By empyrean
Thanks again. But the delimiters are not aligning...
Thanks again. But the delimiters are not aligning i mean the heading is not in tab delimited format as the results are.. another thing is that the common column is repeating twice. i want it to be in...
2,657
Posted By empyrean
Thankyou , pamu but its printing the headers...
Thankyou , pamu

but its printing the headers in three lines on one file and no headers on other file. see the output below.

123 9a.vcf hy92.vcf hy90.vcf...
2,657
Posted By empyrean
Thank you but this is giving out the headings for...
Thank you but this is giving out the headings for second file only. i want those for first file also. First file contains headings in two rows. Also this script is printing out common column twice.....
2,657
Posted By empyrean
Merge with common column
hi i have two files and i wanted to join them using common column. try to do this using "join" command but that did not help.

File 1:

123 9a.vcf hy92.vcf ...
1,966
Posted By empyrean
this works great !! wow what a explanation !!
this works great !! wow what a explanation !!
2,687
Posted By empyrean
Count and merge using common column
I have the following records from multiple files.


415 A G
415 A G
415 A T
415 A .
415 A .
421 G A
421 G A,C
421 ...
1,918
Posted By empyrean
@agama : Thankyou .. the code works great but...
@agama : Thankyou .. the code works great but only thing is that its not printing in ascending order.

---------- Post updated at 09:22 PM ---------- Previous update was at 09:21 PM ----------
...
1,918
Posted By empyrean
Read column and find differences...
I have this file

427 A C A/C 12
436 G C G/C 12
445 C T C/T 12
447 A G A/G 9
451 T C T/C 5
456 A G A/G 12
493 G A G/A 12


I wanted to read the first column and find all other ids which...
1,966
Posted By empyrean
Thank you for the reply. No, The sequence...
Thank you for the reply.

No, The sequence file is common here.. there will be only one sequence. based on the snp position in the table, we need to modify the particular base and substitute the...
1,966
Posted By empyrean
Modifying a sequence using positions!
Hi.. i have two files one with positions information and another is sequence information. Now i need to read the positions and take the snps at the positions and replace that position base with the...
31,093
Posted By empyrean
Refer this post ...
Refer this post (https://www.unix.com/shell-programming-scripting/61669-delete-n-last-lines-file.html)
1,574
Posted By empyrean
thank you all, Its simple and elegant solutions....
thank you all, Its simple and elegant solutions. All solutions are working great !!
1,574
Posted By empyrean
Merging rows using two common rows.
Hi..

My requirement is simple but unable to get that..

File 1 :

3 415 A G
4 421 G .
39 421 G A
2 421 G A,C
41 427 A .
4 427 A C
42 436 G .
3 436 G C
43 445 C .
2 445 C T...
6,100
Posted By empyrean
@Don Cragun... hank you so much.. It just worked...
@Don Cragun... hank you so much.. It just worked perfect. Exactly the way i wanted. As you said, perfect alignment too.. thank you again

Only one small thing is that its not printing the filenames...
6,100
Posted By empyrean
hmmm.. it was so close to complete and got struck...
hmmm.. it was so close to complete and got struck :(
6,100
Posted By empyrean
Thank you for the help.. i modified the space to...
Thank you for the help.. i modified the space to tab. it doesnt work as i wanted but pretty close. i dont know how to modify that.. so when i used the same data as above, i am getting like this

...
6,100
Posted By empyrean
Read multiple files, parse data and append to a file
Hi..Can anyone suggest a simple way of achieving this. I have several files which ends with extension .vcf . I will give example with two files
In the below files, we are interested in

File 1: ...
4,871
Posted By empyrean
cool.. much clear, easy and very few lines of...
cool.. much clear, easy and very few lines of code.. Thank you rdrtx1
4,871
Posted By empyrean
I am not too familiar with awk. This works...
I am not too familiar with awk.
This works perfect. I would love to understand this code. Can you explain briefly?
Thank you so much for the code
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