text: user16709: In case of Drop-seq, we have paired end data.
  Read 1: Cell code + UMI (unique molecule identifier)
  Read 2: The transcript information
  But I have a problem/doubt with the sample I am working on.
  The sample I am using is the following (Check the "Reads" tab).
  As you know the Drop-seq is "paired-end", we are expected to see two reads for a spot. Although this sample say paired-end, it has only one read per spot.
  For example I can share a link of a different scRNA-seq data where you can properly see two reads for a spot
  Example sample, you need to check the "Reads" tab.
  Where I am going wrong?
  I asked one of the main authors of the paper. The following is the reply I got :
  
  I recommend that you download the aligned BAM files that are hosted in
    the same GEO record. Read 1 is already processed into the cell and UMI
    barcodes and held as custom tags (XC and XM) in the BAM files. The
    cells are already barcode-corrected, so if you use those files, your
    cell barcodes will line up with mine; if you start from FASTQs, they
    will not. For most aligners, you can just use the BAM file as input to
    realign. (It has all reads, even those that did not align.)
  
  But I could not find any "XM" or "XC" keywords in the bam file :(
  To understand his reply you have to be familiar the processing steps of the Drop-seq.
  Looks like they have submitted some kind of processed data. I could not figure out how much the data is processed. I am trying to use the data starting at different processing steps but I could not figure out how much the data is processed.
  
  user4968: I received the following message from the author of another Drop-seq paper:
  
  After much conversation with the folks at the SRA, it appears the SRA
    compression algorithm automatically deletes certain subsets of bam
    tags and does so in cryptic way (in the sense of not alerting the
    uploader). Obviously this is going to be an issue for many single cell
    datasets encoded this way, and I hope the SRA will eventually change
    their system to accommodate.
  
  If you look at the "Download" tab of the same page, there now exists a link to download the originally uploaded BAM file.
  Alternately, you can use the SRA AWS tutorial to download the files on that platform. 
  
original_text: 16709: <p>In case of Drop-seq, we have paired end data.</p>
  
  <p>Read 1: Cell code + UMI (unique molecule identifier)</p>
  
  <p>Read 2: The transcript information</p>
  
  <p>But I have a problem/doubt with the sample I am working on.</p>
  
  <p>The sample I am using is the <a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6261587" rel="nofollow noreferrer">following</a> (Check the "Reads" tab).</p>
  
  <p>As you know the Drop-seq is "paired-end", we are expected to see two reads for a spot. Although this sample say paired-end, it has only one read per spot.</p>
  
  <p>For example I can share a link of a different scRNA-seq data where you can properly see two reads for a spot</p>
  
  <p><a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8086553" rel="nofollow noreferrer">Example sample</a>, you need to check the "Reads" tab.</p>
  
  <p>Where I am going wrong?</p>
  
  <p>I asked one of the main authors of the paper. The following is the reply I got :</p>
  
  <blockquote>
    <p>I recommend that you download the aligned BAM files that are hosted in
    the same GEO record. Read 1 is already processed into the cell and UMI
    barcodes and held as custom tags (XC and XM) in the BAM files. The
    cells are already barcode-corrected, so if you use those files, your
    cell barcodes will line up with mine; if you start from FASTQs, they
    will not. For most aligners, you can just use the BAM file as input to
    realign. (It has all reads, even those that did not align.)</p>
  </blockquote>
  
  <p>But I could not find any "XM" or "XC" keywords in the bam file :(</p>
  
  <p>To understand his reply you have to be familiar the <a href="https://github.com/broadinstitute/Drop-seq/files/2425535/Drop-seqAlignmentCookbookv1.2Jan2016.pdf" rel="nofollow noreferrer">processing steps of the Drop-seq</a>.</p>
  
  <p>Looks like they have submitted some kind of processed data. I could not figure out how much the data is processed. I am trying to use the data starting at different processing steps but I could not figure out how much the data is processed.</p>
   4968: <p>I received the following message from the author of another Drop-seq paper:</p>
  
  <blockquote>
    <p>After much conversation with the folks at the SRA, it appears the SRA
    compression algorithm automatically deletes certain subsets of bam
    tags and does so in cryptic way (in the sense of not alerting the
    uploader). Obviously this is going to be an issue for many single cell
    datasets encoded this way, and I hope the SRA will eventually change
    their system to accommodate.</p>
  </blockquote>
  
  <p>If you look at the "Download" tab of the <a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6261587" rel="nofollow noreferrer">same page</a>, there now exists a link to download the originally uploaded BAM file.</p>
  
  <p>Alternately, you can use the <a href="https://www.ncbi.nlm.nih.gov/sra/docs/sra-aws-download/" rel="nofollow noreferrer">SRA AWS tutorial</a> to download the files on that platform. </p>
  