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2 hours ago by

Hi, I have some problems about align GEO data.

How Can I align my GEO's fastq data to gene annotation file(GTF file)
For example, SRR11804718(trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11804718) data,
writers are used dropTag(in dropEst) and they make read1, read2 by Seq-Well protocol. Therefore, read1 has barcode + UMI = 21 length sequence, read2 has 50 length mRNA sequence. just like above(SRR11804718).

The problem is, when I used STAR aligner, it arised error: read1(21) is too shorter then read2(50). I think STAR which accept read1, read2 are paired data(like bulk RNA seq). So, How can I put these data right way? read 1 has only barcode and UMI information and in my opinion, this information is really important for align single cell RNA seq data(fastq) -> ref genome.

In SRR11804718 data, they use dropTag(in dropEst) to bcl -> fastq / and they use Seq-Well protocol. Please help me. How can I make bam file by aligning scRNA-seq data by using STAR right way?


Best regards

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modified 1 hour ago

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Rob4.1k

written
2 hours ago
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dhkwnr950



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