old delete
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
There is probably a better way but here are a couple of commands you will probably find useful and can play with to accomplish your goal. This will take the barcode from the header and put it at the end of the read, thus allowing you to analyze as you normally would. I'm not much of a computer person either but I had to google around a little while ago to figure this type of thing out for a different purpose.
sed -n '1,${p;n;}' [file] > odd_lines
sed -n '2,${p;n;}' [file] > even_lines
The odd_lines file will have the headers and the even_lines file will have the reads. Then, cut the odd_lines file to abstract the barcode.
cut -f2 -d # odd_lines > part_1
cut -f1 -d / part_1 > barcodes
Then paste the barcodes to the ends of the reads and get rid of the tabs that will be between them:
paste even_lines barcodes | tr -d '\011' > reads_with_barcodes
Then put the header part lines together without the barcodes:
cut -f1 -d # odd_lines > first_head
cut -f2 -d / odd_lines > second head
paste first_head second_head | tr '\t' '#/' > headers_without_barcodes
and then finally put the two files back together:
paste headers_without_barcodes reads_with_barcodes | tr '\t' '\n' > new_file_to_analyze
This should work, although there may be typos.
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 11:49 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
Yesterday, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
61 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Comment