Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bam file missing barcode and UMI info

    Hi,

    I used STARsolo but my bam files, below, are missing barcode and UMI info:

    ```
    (/scratch/work/malonzm1/.conda_envs/scvi-env) [malonzm1@login3]/scratch/cs/pan-autoimmune/data/star/scRNAseq/GSE151177/SRR11848679% samtools view SRR11848679Aligned.out.bam|head -n5
    NB500961:910:HJ5TWBGXC:1:23304:10007:9225 0 chr1 6100902 255 55M * 0 0 TTCGGAGCCCCCACTGTTTCCCACTCAGCTTTGTGCTCAGATCCCAGGTCCCAAG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE NH:i:1 HI:i:1 AS:i:54 nM:i:0 NM:i:0 MD:Z:55 jM:B:c,-1 jI:B:i,-1
    NB500961:910:HJ5TWBGXC:1:13111:23716:1741 0 chr1 6100902 255 4S51M * 0 0 GAGATTCGGAGCCCACACTGTTTCCCACTCAGCTTTGTGCTAATATCCAAGGTCC ///AA/EEE/AEEE//AE/////E/<A<EE/E/AE///E/E/A/EEE</A<AA// NH:i:1 HI:i:1 AS:i:42 nM:i:4 NM:i:4 MD:Z:10C26C1G4C6 jM:B:c,-1 jI:B:i,-1
    NB500961:910:HJ5TWBGXC:1:22211:15746:1375 0 chr1 6100902 255 55M * 0 0 TTCGGAGCCCCCACTGTTTCCCACTCAGCTTTGTGCTCAGATCCCAGGTCCCAAG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE NH:i:1 HI:i:1 AS:i:54 nM:i:0 NM:i:0 MD:Z:55 jM:B:c,-1 jI:B:i,-1
    NB500961:910:HJ5TWBGXC:1:13309:24262:17947 0 chr1 6100903 255 55M * 0 0 TCGGAGCCCCCACTGTTTCCCACTCAGCTTTGTGCTCAGATCCCAGGTCCCAAGG AAAAAEAAA/EAEEEEEEE/EEEEEEEEEEEEEEEEAEAEEAEEEEEEEEEEEEE NH:i:1 HI:i:1 AS:i:54 nM:i:0 NM:i:0 MD:Z:55 jM:B:c,-1 jI:B:i,-1​
    ```

    I used the following script:

    ```

    'STAR --outSAMattributes All --outSAMtype BAM Unsorted --quantMode GeneCounts --readFilesCommand gunzip -c --runThreadN %s --sjdbGTFfile %s --outReadsUnmapped Fastx --outMultimapperOrder Random --genomeDir %s --readFilesIn %s %s --outFileNamePrefix %s --soloType CB_UMI_Simple --soloBarcodeReadLength 0 --soloCBwhitelist %s --soloUMIlen %s --soloCBlen %s --soloUMIstart %s'%(NCPU, GTFFILE, GENOMEDIR, infile2, infile1, OUTPREFIX, whitelist, soloumilen, solocblen, soloumistart)
    ```

    Please advise.

    Thanks and good day.

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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 11:49 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-24-2024, 08:47 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
62 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
60 views
0 likes
Last Post seqadmin  
Working...
X