User: linjc.xmu
linjc.xmu • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Last seen:
- 8 months, 4 weeks ago
- Joined:
- 3 years, 9 months ago
- Email:
- l********@gmail.com
Posts by linjc.xmu
<prev
• 23 results •
page 1 of 3 •
next >
0
votes
1
answer
538
views
1
answers
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.xmu • 10
0
votes
1
answer
538
views
1
answers
Comment:
C: Umi tools dedup output
... > umi_tools dedup -I my.sort.bam -S my.dedup.bam ...
written 10 months ago by
linjc.xmu • 10
0
votes
1
answer
538
views
1
answers
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.xmu • 10
0
votes
1
answer
538
views
1
answers
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.xmu • 10
5
votes
1
answer
538
views
1
answer
... 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 ...
0
votes
0
answers
142
views
0
answers
... 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. ...
written 11 months ago by
linjc.xmu • 10
0
votes
0
answers
1.0k
views
0
answers
... 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.xmu • 10
3
votes
0
answers
1.0k
views
0
answers
... 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
...
0
votes
0
answers
536
views
0
answers
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.xmu • 10
2
votes
0
answers
536
views
0
answers
... 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 17 months ago by
linjc.xmu • 10
Latest awards to linjc.xmu
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1355 users visited in the last hour