|
|
Sponsored Content
Top Forums
Shell Programming and Scripting
Extraction of upstream and downstream regions from long sequence file
Post 302951413 by Scrutinizer on Thursday 6th of August 2015 03:30:34 AM
|
|
10 More Discussions You Might Find Interesting
1. Programming
Hi,
I'm working hard on SQL and I came across a hurdle I'm hoping you can help me out with.
I have two tables
table1
headers: chrom start end name score strand
11 9720685 9720721 U0 0 +
21 9721043 9721079 U0 0 -
1 9721093 9721129 U0 0 +
20 ... (2 Replies)
Discussion started by: labrazil
2 Replies
2. Shell Programming and Scripting
Hi all,
I have difficulty to solve the followign problem.
mydata:
StartPoint EndPoint
22 55
2222 2230
33 66
44 58
222 240
11 25
22 60
33 45
The union of above... (2 Replies)
Discussion started by: phoeberunner
2 Replies
3. UNIX for Dummies Questions & Answers
Hi everyone,
I have a large text file containing DNA sequences in fasta format as follows:
>someseq
GAACTTGAGATCCGGGGAGCAGTGGATCTC
CACCAGCGGCCAGAACTGGTGCACCTCCAG
GCCAGCCTCGTCCTGCGTGTC
>another seq
GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT
GACATTTTCATTACTACCATTTTGGAGTACA
>seq3450... (4 Replies)
Discussion started by: Fahmida
4 Replies
4. UNIX for Dummies Questions & Answers
Hi, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2.
Based on a post elsewhere, I found the code:
awk... (2 Replies)
Discussion started by: pathunkathunk
2 Replies
5. Shell Programming and Scripting
Hi all,
I have a file like this
ID 3BP5L_HUMAN Reviewed; 393 AA.
AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 05-SEP-2012, entry version 71.
FT COILED 59 140 ... (1 Reply)
Discussion started by: manigrover
1 Replies
6. Shell Programming and Scripting
FILE_ID extraction from file name and save it in CSV file after looping through each folders
My files are located in UNIX Server, i want to extract file_id and file_name from each file .and save it in a CSV file. How do I do that?
I have folders in unix environment, directory structure is... (15 Replies)
Discussion started by: princetd001
15 Replies
7. Shell Programming and Scripting
Hi I have 2 files; usually the end position in the file1 is the start position in the file2 and the end position in file2 will be the start position in file1 (flanks)
file1
Id start end
aaa1 0 3000070
aaa1 3095270 3095341
aaa1 3100822 3100894
aaa1 ... (1 Reply)
Discussion started by: anurupa777
1 Replies
8. IP Networking
Old skool UNIX and Linux geek here, but newbie to the world of DNS and bind. I've recently been tasked with replacing our DNS infrastructure, currently on Windows, with a RHEL based solution. And I assume that means using bind, which I've not used before. Here's my question:
Suppose our company... (3 Replies)
Discussion started by: lupin..the..3rd
3 Replies
9. Shell Programming and Scripting
HI,
I have a Complete genome fasta file and I have list of sub sequence regions
in the format as :
4353..5633
6795..9354
1034..14456
I want a script which can mask these region in a single complete genome fasta file with the alphabet N
kindly help (2 Replies)
Discussion started by: margarita
2 Replies
10. Shell Programming and Scripting
i want to extract specific region of interest from big file. i have only start position, end position and seq id, see my query is:
I have file1 is this
>GL3482.1
GAACTTGAGATCCGGGGA
GCAGTGGATCTCCACCAG
CGGCCAGAACTGGTGCAC
CTCCAGGCCAGCCTCGTC
CTGCGTGTC
>GL3550.1... (14 Replies)
Discussion started by: harpreetmanku04
14 Replies
LEARN ABOUT X11R4
zcmp
ZDIFF(1) General Commands Manual ZDIFF(1) NAME
zcmp, zdiff - compare compressed files SYNOPSIS
zcmp [ cmp_options ] file1 [ file2 ] zdiff [ diff_options ] file1 [ file2 ] DESCRIPTION
Zcmp and zdiff are used to invoke the cmp or the diff program on files compressed via gzip. All options specified are passed directly to cmp or diff. If only file1 is specified, it is compared to the uncompressed contents of file1.gz. If two files are specified, their con- tents (uncompressed if necessary) are fed to cmp or diff. The input files are not modified. The exit status from cmp or diff is pre- served. SEE ALSO
cmp(1), diff(1), zmore(1), zgrep(1), znew(1), zforce(1), gzip(1), gzexe(1) BUGS
Messages from the cmp or diff programs may refer to file names such as "-" instead of to the file names specified. ZDIFF(1)