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  • malonzm1
    started a topic bam file missing barcode and UMI info

    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.

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