User: newbinf

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newbinf0
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Posts by newbinf

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Comment: C: split BAM file with same cell-barcode and UMI pair
... Sorry for the late reply! I am using the 10x cell barcode tags, they are now placed in the read headers. I cut out the tags because I do not want misalignments caused by the cell barcode and UMI tags. ...
written 4 months ago by newbinf0
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Comment: C: split BAM file with same cell-barcode and UMI pair
... There are only about 50 cell barcodes in my gene/region of interest. So it would be about 50-70 files. I should clarify I used samtools to only grab the portion of the bam file with alignments to one gene. ...
written 4 months ago by newbinf0
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split BAM file with same cell-barcode and UMI pair
... I have single cell RNA-seq reads (from 10x Chromium) that have already been pre-processed. The cell-bacode and UMI tag were cut-and-pasted to the header (via umi-tools) and low quality reads were removed. Next, I mapped the reads (with STAR) and isolated the reads from a gene of interest (via samtoo ...
unique molecular identifier rna-seq umi-tools written 4 months ago by newbinf0
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How to extract reads passing a threshold for Mean Sequence Quality
... I have some RNA-seq data that I trimmed and then ran through FastQC to check the quality. For the R2 file for my read, there seems to be a bad quality score for a large portion of the reads. A lot of the reads are in the red zone. ![This shows that the overall quality of the R2 reads are relative ...
rna-seq written 5 months ago by newbinf0 • updated 5 months ago by genomax64k
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Comment: C: How to move UMI tags to the header
... After skimming through the documentation, this looks like what I need. Thank you! ...
written 6 months ago by newbinf0
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How to move UMI tags to the header
... I have complete sequences from 10x Chromium that look like the following: |----my 16 bp cell barcode----|---8bp 10x UMI---|--SO--|-------------------cDNA (100 bp)----------------------| SO = switch oligo The reads are demultiplexed and don't have the Illumina barcodes in the sequence. I want to ma ...
umi alignment rna-seq written 6 months ago by newbinf0
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Amplicon Based Data
... Hi all, I have amplicon-based data where the reads look like this: forward-adapter + 4bp molecular tag + ligation arm (18-24bp) + sequence of interest + extension arm (18-24 bp) + 4bp molecular tag + reverse-adapter I have both forward and reverse reads (R1 and R2) and they are pair-ended. How do ...
sequencing written 7 months ago by newbinf0
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Answer: A: Understanding Annovar Output
... I realize that DP:RD:AD is total reads: reference allele reads: alternative allele reads. Please correct me if I am wrong. How do I isolate these values. Or are there columns in the VCF file output that contain these values already? ...
written 8 months ago by newbinf0
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Understanding Annovar Output
... I have a vcf output from Annovar (and wAnnovar), and need some help understanding all of the headers. I know i am given the reference and the alternative allele. However, I want to know how many reads in my input file were reference and alternative. I'm looking at the vcf file, and see some traili ...
vcf annovar written 8 months ago by newbinf0 • updated 8 months ago by h.mon24k
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Comment: C: Removing Duplicates before aligning
... I want to delete reads with the exact same sequences (including barcodes) so that I can eliminate any PCR duplicates. I want to make sure that my future variant analysis is not biased because of PCR duplicates. ...
written 8 months ago by newbinf0

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