Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • nilshomer
    replied
    Originally posted by jlfmssm View Post
    but I got this:
    [aimin@node01 all_sam_data]$ samtools view -S -X 1382_1.sam/1382_1.sam -o 1382_1_test.out
    [samopen] no @SQ lines in the header.
    [sam_read1] missing header? Abort!
    What I should do now?
    The lines "no @SQ lines in the header" and "missing header?" should tell you to check the header in the SAM file. Is there one? If not, you have to feed in your reference with the "-T" option.

    Leave a comment:


  • jlfmssm
    replied
    but I got this:
    [aimin@node01 all_sam_data]$ samtools view -S -X 1382_1.sam/1382_1.sam -o 1382_1_test.out
    [samopen] no @SQ lines in the header.
    [sam_read1] missing header? Abort!
    What I should do now?

    Leave a comment:


  • nilshomer
    replied
    Originally posted by jlfmssm View Post
    Thanks, I tried, but I got this error:

    [aimin@node01 all_sam_data]$ samtools view -X 1382_1.sam/1382_1.sam
    [bam_header_read] EOF marker is absent.
    [main_samview] fail to read the header.
    Use the "-S" flag to specify that you are inputting a SAM file (not a BAM file). Please read the documentation, including the output when no options/input is specified.

    Leave a comment:


  • jlfmssm
    replied
    Thanks, I tried, but I got this error:

    [aimin@node01 all_sam_data]$ samtools view -X 1382_1.sam/1382_1.sam
    [bam_header_read] EOF marker is absent.
    [main_samview] fail to read the header.

    Leave a comment:


  • nilshomer
    replied
    Originally posted by jlfmssm View Post
    I am new for NGS data.
    How to check reads are properly paired from SAM file?
    It is appreciated someone can point me some programs?

    Thanks,
    Aimin
    Use 'samtools view -X <in.bam>'. All reads with a capital "P" in the flag field are properly paired.

    Leave a comment:


  • How to check read are properly paired from SAM file?

    I am new for NGS data.
    How to check reads are properly paired from SAM file?
    It is appreciated someone can point me some programs?

    Thanks,
    Aimin

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 06-21-2024, 07:49 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-20-2024, 07:23 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-17-2024, 06:54 AM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-14-2024, 07:24 AM
0 responses
27 views
0 likes
Last Post seqadmin  
Working...
X