Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • #1

    output samtools.pl

    Dear users,
    I used BFAST program to generate a file .sam (using microRNA reads from SOLiD ABI).
    I run SAMTOOLS to analyse SNPs and mutations, and I generated at the end two output files:
    a pileup file and a file .snps (by samtools.pl varFilter).

    This is an example of my file .snps:

    g hsa-let-7a-3 61 * */+A 73 73 40 81 * +A 79 2 0 0 0
    g hsa-let-7a-3 63 * */-C 133 133 45 79 * -C 76 1 2 3 1
    g hsa-let-7a-3 64 * */-T 165 165 44 78 * -T 77 1 0 0 0
    g hsa-let-7a-3 68 * */-T 385 385 40 53 * -T 52 1 0 0 0
    g hsa-let-7a-3 70 * */+A 78 78 35 43 * +A 42 1 0 0 0
    D hsa-let-7b 22 * */+A 895 895 22 1717 * +A 1652 36 29 7 37
    D hsa-let-7b 24 * */+TC 14761 14761 23 1728 * +TC 1573 51 104 7 4
    D hsa-let-7b 25 * +TA/+CTA 17955 37444 23 1730 +TA +CTA 32 17 1681 35 18
    D hsa-let-7b 26 * +A/+TA 21497 46739 23 1732 +A +TA 393 162 1177 40 29
    D hsa-let-7b 27 * +A/* 31077 31077 23 1733 +A * 6 1651 76 4 5
    D hsa-let-7b 28 T Y 228 228 23 1736 ,,.+1C,,$C.C...+4ATTC.+4ATTC*.+4ATTCC,.+1C.,...+4ATTCC..+1CCC.+1CC.+4ATTC
    .+1C.+4ATTC.+1C..+4ATTC.+4ATTC.+4ATTCC.+1C*.+4ATTCC.+1CC.+4ATTCC.+1C...+1CCC.+1C.+4ATTCC..+1CC.+1C.+1C.+1C.+1CC.+1C.+4ATTCC.+1C.+1C...+4ATTC.+1C.C..+1C.C
    ..+1C..+1C..+1C.....+4ATTCC.+4ATTCC..+4ATTC..C.+4ATTC.C.+1C.+4ATTCC.+1C.+4ATTCC...+4ATTC.C.+4ATTC.+1C......C.+4ATTC..+1C.+4ATTC.+1C.C.+4ATTC.+1CCCC.+1C.+
    1C.+4ATTC.+1C.+4ATTC.+1C.+4ATTC.+4ATTC.+4ATTC.+1C.+1CC.+4ATTC.+1CCC.+1CC.+1C.+1CC.C.+1CC.+1C.+1C.+4ATTC.+4ATTC..+1C.+1C.+1CCC.+4ATTCC.+1CC.+1C...C.+1C.+1
    CC.+4ATTC..+1C.+1C.+1C.+1C*.+4ATTC..+4ATTC.+1C.+1C.+1C.+1C.+1CC.CC.+4ATTC.+1C.+1CC..+1C..+1C.+1C..+1C.+4ATTC.+1C.+1C.+1C...+1C...+1C.A.+4ATTC.+4ATTC.-1C.
    +3CGC.+2TC.+1C.+1CC.+1C.+4ATTC..+4ATTC.+4ATTCC..+1C.+1C.C.CC.+4ATTCC.+4ATTC.+1C.+1C.+4ATTC.+1CC.C.+1C.+4ATTC.+4ATTC.+4ATTC.+1CC.+4ATTCC.+4ATTC.+4ATTC.+1C
    .+1CCC.+1C.+1C.+1C.+1C.+1CC.+4ATTC.+1CCC.+1CCCC.+1C.+1C.+4ATTC.+1CC.+1C..+4ATTC.CC.+1C.+4ATTC.+1C.CC.+1C.C.+1C.+1C.+1CC.+1CC.+1C.+1C.+1C.+4ATTC.+4ATTC.+1
    C.+4ATTCC.+1C.+1C.+1C.+1C.+1CC.+5CATTC.+4ATTC.+4ATTCCC.+1C.+1C.+1CC..C.+4ATTC.+1C..+1C..+1C.+1CC.+1C*.+1CCC.+4ATTC.+4ATTC..+1C.+1C..+1C..C.+4ATTC.+4ATTC.
    +4ATTC.C.+4ATTC.+1CC..+1C.+1CC.+4ATTC.+1C.+1C.CCC.+1C.+1C.+4ATTC.+4ATTC.+1C.+1CC..-1CC.+1C.+1C.+1C..+1C.+1C..+1C*...+1CC.+1C...+4ATTC.+1C.+1CC..+4ATTC..+
    1C...+1CC.+1C.+1C..C.+1C.-2CACC..C..+4ATTCA.+1C..+1C.+4ATTC..+1C.+1C..+1CC.+4ATTC.+4ATTC.+1C.+1C..+6GTATTCC.C.+4ATTC.+1C..+1C.+4ATTC.+4ATTC.+4ATTCC.

    But I don't know how I can read this file. What correspond to each column?
    How or where can I find the number of reads (the number of count of miRNA in the alignment)?

    Thanx a lot!
    Bye
    M.Elena
    Tags: None
  • #2
    Originally posted by m_elena_bioinfo View Post
    Dear users,
    I used BFAST program to generate a file .sam (using microRNA reads from SOLiD ABI).
    I run SAMTOOLS to analyse SNPs and mutations, and I generated at the end two output files:
    a pileup file and a file .snps (by samtools.pl varFilter).

    This is an example of my file .snps:

    g hsa-let-7a-3 61 * */+A 73 73 40 81 * +A 79 2 0 0 0
    g hsa-let-7a-3 63 * */-C 133 133 45 79 * -C 76 1 2 3 1
    g hsa-let-7a-3 64 * */-T 165 165 44 78 * -T 77 1 0 0 0
    g hsa-let-7a-3 68 * */-T 385 385 40 53 * -T 52 1 0 0 0
    g hsa-let-7a-3 70 * */+A 78 78 35 43 * +A 42 1 0 0 0
    D hsa-let-7b 22 * */+A 895 895 22 1717 * +A 1652 36 29 7 37
    D hsa-let-7b 24 * */+TC 14761 14761 23 1728 * +TC 1573 51 104 7 4
    D hsa-let-7b 25 * +TA/+CTA 17955 37444 23 1730 +TA +CTA 32 17 1681 35 18
    D hsa-let-7b 26 * +A/+TA 21497 46739 23 1732 +A +TA 393 162 1177 40 29
    D hsa-let-7b 27 * +A/* 31077 31077 23 1733 +A * 6 1651 76 4 5
    D hsa-let-7b 28 T Y 228 228 23 1736 ,,.+1C,,$C.C...+4ATTC.+4ATTC*.+4ATTCC,.+1C.,...+4ATTCC..+1CCC.+1CC.+4ATTC
    .+1C.+4ATTC.+1C..+4ATTC.+4ATTC.+4ATTCC.+1C*.+4ATTCC.+1CC.+4ATTCC.+1C...+1CCC.+1C.+4ATTCC..+1CC.+1C.+1C.+1C.+1CC.+1C.+4ATTCC.+1C.+1C...+4ATTC.+1C.C..+1C.C
    ..+1C..+1C..+1C.....+4ATTCC.+4ATTCC..+4ATTC..C.+4ATTC.C.+1C.+4ATTCC.+1C.+4ATTCC...+4ATTC.C.+4ATTC.+1C......C.+4ATTC..+1C.+4ATTC.+1C.C.+4ATTC.+1CCCC.+1C.+
    1C.+4ATTC.+1C.+4ATTC.+1C.+4ATTC.+4ATTC.+4ATTC.+1C.+1CC.+4ATTC.+1CCC.+1CC.+1C.+1CC.C.+1CC.+1C.+1C.+4ATTC.+4ATTC..+1C.+1C.+1CCC.+4ATTCC.+1CC.+1C...C.+1C.+1
    CC.+4ATTC..+1C.+1C.+1C.+1C*.+4ATTC..+4ATTC.+1C.+1C.+1C.+1C.+1CC.CC.+4ATTC.+1C.+1CC..+1C..+1C.+1C..+1C.+4ATTC.+1C.+1C.+1C...+1C...+1C.A.+4ATTC.+4ATTC.-1C.
    +3CGC.+2TC.+1C.+1CC.+1C.+4ATTC..+4ATTC.+4ATTCC..+1C.+1C.C.CC.+4ATTCC.+4ATTC.+1C.+1C.+4ATTC.+1CC.C.+1C.+4ATTC.+4ATTC.+4ATTC.+1CC.+4ATTCC.+4ATTC.+4ATTC.+1C
    .+1CCC.+1C.+1C.+1C.+1C.+1CC.+4ATTC.+1CCC.+1CCCC.+1C.+1C.+4ATTC.+1CC.+1C..+4ATTC.CC.+1C.+4ATTC.+1C.CC.+1C.C.+1C.+1C.+1CC.+1CC.+1C.+1C.+1C.+4ATTC.+4ATTC.+1
    C.+4ATTCC.+1C.+1C.+1C.+1C.+1CC.+5CATTC.+4ATTC.+4ATTCCC.+1C.+1C.+1CC..C.+4ATTC.+1C..+1C..+1C.+1CC.+1C*.+1CCC.+4ATTC.+4ATTC..+1C.+1C..+1C..C.+4ATTC.+4ATTC.
    +4ATTC.C.+4ATTC.+1CC..+1C.+1CC.+4ATTC.+1C.+1C.CCC.+1C.+1C.+4ATTC.+4ATTC.+1C.+1CC..-1CC.+1C.+1C.+1C..+1C.+1C..+1C*...+1CC.+1C...+4ATTC.+1C.+1CC..+4ATTC..+
    1C...+1CC.+1C.+1C..C.+1C.-2CACC..C..+4ATTCA.+1C..+1C.+4ATTC..+1C.+1C..+1CC.+4ATTC.+4ATTC.+1C.+1C..+6GTATTCC.C.+4ATTC.+1C..+1C.+4ATTC.+4ATTC.+4ATTCC.

    But I don't know how I can read this file. What correspond to each column?
    How or where can I find the number of reads (the number of count of miRNA in the alignment)?

    Thanx a lot!
    Bye
    M.Elena
    I assume you are having problems understanding the samtools pileup output and BFAST ran fine. Take a look at these two pages on the samtools website that explain the output format:

    Pileup Format
    http://samtools.sourceforge.net/pileup.shtml

    Consensus/Indel Calling
    http://samtools.sourceforge.net/cns0.shtml

    Comment

    • #3
      I guess you are using "samtools.pl -p" which explains why your variants get filtered out. The first letter gives the reason:

      # d low depth
      # D high depth
      # W too many SNPs in a window (SNP only)
      # G close to a high-quality indel (SNP only)
      # Q low RMS mapping quality (SNP only)
      # g close to another indel with higher quality (indel only)

      Note that if a SNP is filtered out due to depth, it will not be tested with "G".

      Comment

      Previous template Next

      Latest Articles

      Collapse
      • seqadmin
        Essential Discoveries and Tools in Epitranscriptomics
        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...
        04-22-2024, 07:01 AM
      • 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
      View All

      ad_right_rmr

      Collapse

      News

      Collapse
      Topics Statistics Last Post
      Expanding the Horizons of Cellular Research with the Single Cell Atlas by seqadmin
      Started by seqadmin, Today, 11:49 AM
      0 responses
      8 views
      0 likes
      		 Last Post seqadmin
      by seqadmin
      Today, 11:49 AM  
      Genetic Variants and Diabetes Risk in Childhood Cancer Survivors by seqadmin
      Started by seqadmin, Yesterday, 08:47 AM
      0 responses
      16 views
      0 likes
      		 Last Post seqadmin
      by seqadmin
      Yesterday, 08:47 AM  
      Cancer Metastasis: A Deep Dive into Cellular Plasticity by seqadmin
      Started by seqadmin, 04-11-2024, 12:08 PM
      0 responses
      61 views
      0 likes
      		 Last Post seqadmin
      by seqadmin
      04-11-2024, 12:08 PM  
      Proteogenomic Profiles Offer New Clues in Prostate Cancer by seqadmin
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      60 views
      0 likes
      		 Last Post seqadmin
      by seqadmin
      04-10-2024, 10:19 PM  
      View All
      Working...
      X