Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • How to reverse complement the nuclotides, if the coordinates are in reverse order?

    I have the series of coordinates in id.txt file, whose coordinates sequences are in genome.fasta file. The coordinates of id.txt file is shown below,
    Contig3:15-7
    Contig2:5-10
    Contig1:12-3

    The genome.fasta file is shown below,
    >Contig1
    AAGGCCATCAAGGACGTGGATGAGGTCGTCAAG
    >Contig2
    ACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCC
    >Contig3
    GCTGCGGCGCTGATCCTGGCGGCCCGCGCCGAG

    I have used the following codes to extract the sequences from genome.fasta based on the coordinates in <id.txt> by using the following command <xargs samtools faidx genome.fasta <id.txt > result.fasta> It has extracted only <Contig2:5-10sequence>. Because, the coordinates of <Contig2:5-10> is in proper order. But <Contig3:15-7> and <Contig1:12-3> coordinates are in reverse order, So samtools could not fetch those sequences.

    I need to extract those sequences from <Contig2:5-10> and <Contig3:15-7> coordinates and also I want to reverse complement them. I have larger fasta file and plenty of coordinates sequences to be extracted, So I need to automate this process. So, please help me to automate this process. Thank you in advance.

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    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...
    04-04-2024, 04:25 PM
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
18 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
22 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Working...
X