User: linjc.xmu

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linjc.xmu10
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3 years, 9 months ago
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Posts by linjc.xmu

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Umi tools dedup output
... UMI is 10 nt long. Each sample contains ~20M 75 bp reads (include UMI) Arabidopsis sample. This was generated by 18 cycles PCR. I got dedup result for the other data (also ~20M reads), which was generated by 30 cycles PCR. ...
written 10 months ago by linjc.xmu10
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Comment: C: Umi tools dedup output
... > umi_tools dedup -I my.sort.bam -S my.dedup.bam ...
written 10 months ago by linjc.xmu10
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Comment: C: Umi tools dedup output
... I used sorted and indexed BAM for dedup on cluster, but it stopped at some point. > 2019-07-31 19:40:04,781 INFO Written out 6400000 reads > > 2019-07-31 19:41:47,464 INFO Written out 6500000 reads > > 2019-07-31 19:44:46,081 INFO Written out 6600000 reads > > 2019-07-31 19: ...
written 10 months ago by linjc.xmu10
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Comment: C: Umi tools dedup output
... My data is single end. When I use SAM for dedup (without sorting), it produces almost the same size as input. When I use sorted and index BAM, the output is about 10% of input BAM. But during BAM file dedup, RAMs are collapsed (I have 4X8GB RAMs, now only left 1 after 2 times running BAM dedup). My ...
written 10 months ago by linjc.xmu10
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Umi tools dedup output
... Hi. Does anyone use UMItools for remove reads duplication? I ran dedup scripts and output 3 files, xxx_edit_distance.tsv, xxx_per_umi.tsv and xxx_per_position.tsv. If I want to calculate how many unique read I got (after removing duplication) and how many UMI/gene, which file and which column should ...
umitools written 10 months ago by linjc.xmu10 • updated 10 months ago by i.sudbery7.7k
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Bisulfate sequencing data
... Hi, all. I have CG.bw, CHH.bw and CHG.bw bisulfate sequencing data. I need to calculate the methylation level of each types around a certain regions stored in a bed file. Are there any tools have this function? Thanks a lot. ...
bisufate sequencing sequencing written 11 months ago by linjc.xmu10
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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 13 months 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 13 months ago by linjc.xmu10 • updated 13 months ago by genomax83k
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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 17 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 17 months ago by linjc.xmu10

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Popular Question 11 months ago, created a question with more than 1,000 views. For STAR --quantMode GeneCounts function
Popular Question 17 months ago, created a question with more than 1,000 views. For RNA-seq library/Gel purification/bioanalyzer

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