How to remove header's tail of a multi-fasta file with sed or other
Hi!
I have a multifasta file with read's headers such as:
>ITS1F_A_B10_R_2014_04_24_15_26_33_user_SN2-26_Run_2_for_its_oom_and_phyg_run2withbarcode.fastq_VG6RM_00181_00132
CCTGCGGAAGGATCATTAATGAAAATGTGTTGCCGGGGCCCATAATCCCGGCACTAACCTTCTTATCCATAACACCTGTGCACTGTTGGATGCTTGCATCCACTTTTATACTAAACAATTTGTAACAAATGTAGTCTTATTATAATTAATAAAACTTTTAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC
>ITS1F_A_B10_R_2014_04_24_15_26_33_user_SN2-26-Run_2_for_its_oom_and_phyg_run2withbarcode.fastq_VG6RM_00171_00907
CCTGCGGAAGGATCATTACCGAGTTAGGGTCCTCTGGGGCCGAACCTCCCAACCCTGTGTCTATTGTTACCTTTTAGTTGCTTCGGCGGGCCGGCCGTCCTGACCAACTGGTCTCGCCGGCCGCCGGTCGTGGGTCTCCACGA
now, I would like to remove this tail part of my hearders where we get the sequence's id. I do not know how to do so for different tails for each reads.I thought of something like this:
sed s'/^.fastq/s/[^ ]* //'g
but it does not apply for some reason.
I would like to get something like this:
>ITS1F_A_B10_R_2014_04_24_15_26_33_user_SN2-26_Run_2_for_its_oom_and_phyg_run2withbarcode.fastq
CCTGCGGAAGGATCATTAATGAAAATGTGTTGCCGGGGCCCATAATCCCGGCACTAACCTTCTTATCCATAACACCTGTGCACTGTTGGATGCTTGCATCCACTTTTATACTAAACAATTTGTAACAAATGTAGTCTTATTATAATTAATAAAACTTTTAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC
>ITS1F_A_B10_R_2014_04_24_15_26_33_user_SN2-26-Run_2_for_its_oom_and_phyg_run2withbarcode.fastq
CCTGCGGAAGGATCATTACCGAGTTAGGGTCCTCTGGGGCCGAACCTCCCAACCCTGTGTCTATTGTTACCTTTTAGTTGCTTCGGCGGGCCGGCCGTCCTGACCAACTGGTCTCGCCGGCCGCCGGTCGTGGGTCTCCACGA
• 3,764 views
•
link
updated
by
Ram
•
written
by
tremblayemilie9 •
•
written
by
tremblayemilie9 •
2 answers
OH!!!!!!!!
THAT WORKS :D:D:D:D
thank you so much :D
Awesome !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
• 0 views
•
link
written
by
tremblayemilie9 •
Log in to answer this question.
More posts like this
-
Remove whitespaces on fasta files, except on fasta-header
written by genomes_and_MGEs •
-
Append characters to end of fasta sequences in a multifasta file
written by sid5427 •
-
Remove Extra Info From Fasta Header
written by kbeavers97 •
-
Remove duplicates from fasta keeping at least one sequence per group based on header
written by vixelaa •
-
File not suitable for fasta index generation.
written by ja4123 •
-
Removing the last part of fasta header in many alignmnet files
written by Badh2 •
-
Change NCBI fasta file headers to makeblastdb format
written by chland •
-
How to compare the similarity of a dataset against a larger dataset and plot a heat map?
written by nattzy94 •
-
Trim FASTA header in multifasta file
written by j.m.carsten •
-
remove part of a multifasta header with sed or other
written by tremblayemilie9 •
Hi again,
I also have to remeve that sequence number from another file, but in that case, the sequence is in between...:
So I want to keep the
size=52893part but remove the72JCK_00944_01804part.You might wanna start working on regular expressions more. These come best when you practice a bit. As long as you don't overwrite the file, nothing should go wrong in experimentation.
In this case, you wanna match something that starts after a
fastq_and ends before the next;Should be easy enough to do that from the answer in your other question on the forum.
Hey I want to remove the header from a multifasta file except the first header is that possible?
This is not an answer to the top-level question and hence must not be added as an answer. I'm moving it to a comment.
Please open a new post describing your exact problem as well as what you've tried in your efforts to solve that problem.