Unconfigured Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • mediator
    Member
    • Nov 2010
    • 27

    samtools sort bam file error: generate non-existent file

    Hi,
    The following is the shell script I wrote to use samtools for sorting bam files. The bam files are from pair end Tophat alignment.

    #!/bin/sh
    samtools sort /data/N1.bam /data/N1_sorted
    .
    .
    .
    .
    The script seemed run OK. But when I do ls -l under the output directory, all the sorted file has a ? inside its file name, like N1_sorted?.bam. Those sorted files are there, except I could not download nor edit them. Any suggestions? Thanks.

Latest Articles

Collapse

  • GATTACAT
    Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
    by GATTACAT
    Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
    07-01-2026, 11:43 AM
  • SEQadmin2
    Nine Things a Sample Prep Scientist Thinks About Before Sequencing
    by SEQadmin2


    I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

    Here are nine questions we think about, in roughly the order they matter, before...
    06-18-2026, 07:11 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, Yesterday, 11:05 AM
0 responses
7 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 07-02-2026, 11:08 AM
0 responses
28 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 06-30-2026, 05:37 AM
0 responses
27 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 06-26-2026, 11:10 AM
0 responses
27 views
0 reactions
Last Post SEQadmin2  
Working...