User: linjc.xmu
linjc.xmu • 10
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Posts by linjc.xmu
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... 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.xmu • 10
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... 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
...
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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.xmu • 10
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... 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 ...
written 5 months ago by
linjc.xmu • 10
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... 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 ...
written 5 months ago by
linjc.xmu • 10
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... 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 ...
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... 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. ...
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... Thanks. Do you mean it's better to get data from Undetermined one? ...
written 8 months ago by
linjc.xmu • 10
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... 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.xmu • 10
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... Thanks. Sequencing company said Novaseq generates a GGGGGG index file (reads) naturally. What's this? ...
written 8 months ago by
linjc.xmu • 10
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