User: linjc.xmu

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linjc.xmu10
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Posts by linjc.xmu

<prev • 17 results • page 1 of 2 • next >
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Comment: C: fast-dump of 10x genomics SRA data
... I think seq ID should be equal for one cell barcode/UMI and one sequence in read 2. Is there any way to repair the pair? ...
written 4 weeks ago by linjc.xmu10
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fast-dump of 10x genomics SRA data
... Dear all, I used fastq-dump to extract single cell SRA data of 10X genomics. But the sequences ID are seemed not paired between read1 and read2. Did anyone meet with this problem? > fastq-dump --split-files --origfmt SRR8315908.sra Rejected 105369008 READS because READLEN < 1 ...
sequence written 4 weeks ago by linjc.xmu10 • updated 4 weeks ago by genomax67k
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Comment: C: bedtools genomecov -scale problem
... Thanks. head a.bed Chr1 5846 5847 1 PAreal + Chr1 5847 5848 1 PAreal + Chr1 5851 5852 1 PAreal + Chr1 5861 5862 1 PAreal + Chr1 5893 5894 1 PAreal + Chr1 5894 5895 1 PAreal + Chr1 5896 5997 400 PAreal + Chr1 6790 6791 10 PAreal - Chr1 6792 6793 1 PAreal - Ch ...
written 5 months ago by linjc.xmu10
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bedtools genomecov -scale problem
... Deal all, I am using bedtools to produce a bedgraph from bed file. a.bed is: Chr1 5846 5847 1 Chr1 5851 5852 1 Chr1 5861 5862 2 Then I use: bedtools genomecov -bg -strand + -i a.bed -scale unscaled -g chrom.size > a.bedgraph This will change the column 3 into 0. If I use: b ...
software error written 5 months ago by linjc.xmu10
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filter internal priming events in oligdT based Reverse transcription of 3'end library
... Hi. Is there any way to use samtools or bedtools to filter internal priming from BAM file? The principle is: within -10 nt and +10 nt window of the first base of unique mapped reads, if there has AAAAA (five continuous As or more than five As), this read should be filter out from BAM file. Thank you ...
rna-seq written 5 months ago by linjc.xmu10
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STAR set --sjdbOverhang value
... Dear all, STAR manual said set --sjdbOverhang at readlength-1. I am confused by this with two questions. 1. If I generated genome index by setting it at 100 previously, and now I have a PE150 reads, should I re-generate genome index by setting it at --sjdbOverhang 149? 2. If I use --clip3pNbases 5 ...
rna-seq written 8 months ago by linjc.xmu10 • updated 8 months ago by swbarnes25.5k
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STAR --quantMode GeneCounts function
... Dear all, Does STAR 2.6 `--quantMode GeneCounts` only quant unique mapping reads? How to specialize it only quant the unique mapped reads? Thanks a lot. ...
rna-seq written 8 months ago by linjc.xmu10 • updated 8 months ago by RamRS21k
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Comment: C: De-multiplex of no illumina index RNAseq libraries on Novaseq
... Thanks. Do you mean it's better to get data from Undetermined one? ...
written 8 months ago by linjc.xmu10
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Comment: C: De-multiplex of no illumina index RNAseq libraries on Novaseq
... Yes. The barcode location is right. My insertion size is ~180-375 bp. Read length is PE150. Sequencing facility sent me G8 data split by my barcode. But the unique mapping rate is low (~47%), multi-alignment rate is ~50%. Usually, I got 90% unique mapping for arabidopsis samples on Hiseq2500. So I a ...
written 8 months ago by linjc.xmu10
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Comment: C: De-multiplex of no illumina index RNAseq libraries on Novaseq
... Thanks. Sequencing company said Novaseq generates a GGGGGG index file (reads) naturally. What's this? ...
written 8 months ago by linjc.xmu10

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Popular Question 4 months ago, created a question with more than 1,000 views. For RNA-seq library/Gel purification/bioanalyzer

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