User: younglin113
younglin113 • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 1 year, 10 months ago
- Email:
- y**********@gmail.com
Posts by younglin113
<prev
• 26 results •
page 1 of 3 •
next >
1
vote
0
answers
77
views
0
answers
... Hello everyone,
Recently, I am dealing with a batch of BS-seq based single-base resolution DNA methylation data. But I got into this trouble:
for the same sample, since the sequencing depth was not enough in the first time, so we added another sequencing procedure. And now I want to analy ...
written 12 weeks ago by
younglin113 • 40
3
votes
0
answers
114
views
0
answers
... I recently read an article about SNPs analysis. And I cannot find out how they did the process.
Here is the description in this article:
INRICH was used to infer the relationship between H4K16ac changes and PLINK-joined AD GWAS SNP intervals (linkage due to HapMap release 23) using standard paramet ...
written 3 months ago by
younglin113 • 40
• updated
7 weeks ago by
Biostar ♦♦ 20
0
votes
2
answers
358
views
2
answers
... Thanks a lot. It's really helped my doubts. ...
written 11 months ago by
younglin113 • 40
0
votes
2
answers
358
views
2
answers
... Oh, so it is. Thanks a lot. So I just need to change the header and it can sort as I want it to, is that what you mean ? ...
written 11 months ago by
younglin113 • 40
2
votes
2
answers
358
views
2
answers
... Recently, I was doing an RNA-seq project, and I used spike-in control sequences in my experiment. So I mapped the reads to both human genome and spike-in sequences. And I successfully got the bam file, but when I tried to use the command `samtools sort -o aa_sorted.bam aa.bam` to sort the bam file a ...
written 11 months ago by
younglin113 • 40
• updated
11 months ago by
finswimmer ♦ 13k
0
votes
0
answers
457
views
0
answers
... Yes, the bam file contains the GLuc and CLuc sequences. And the two genes in my gtf file is not the same. They are "GLuc" and "CLuc", just look similar in this picture. And the bam file shows like this :
![enter image description here][1]
[1]: https://i.ibb.co/cLQC17X/TIM-20190322213501.png ...
written 11 months ago by
younglin113 • 40
0
votes
0
answers
457
views
0
answers
... Because the spike-in sequences I used is not exactly the Thermofisher version. And the gtf file I made up seems really normal, right? ...
written 11 months ago by
younglin113 • 40
0
votes
0
answers
457
views
0
answers
... Here is the situation:
I want to count the reads number of spike-in sequences of an RNA-seq project. And I already mapped the reads to both the human genome and spike-in sequences, and got the bam files. Then I tried to use featurecounts tool to quantify the reads number of both genes and spike-in s ...
written 11 months ago by
younglin113 • 40
• updated
9 months ago by
Biostar ♦♦ 20
0
votes
1
answer
879
views
1
answers
... I tried the `samtools view -F 256` command, and the number of rows of the output file equals the clean reads number. So this command actually only output the multiple mapping reads for once, rather than filter out those multiple mapping reads, doesn't it?
And here is the exact number of a sample:
cl ...
written 11 months ago by
younglin113 • 40
0
votes
1
answer
879
views
1
answers
... The overrepresented sequences are :![enter image description here][1]
[1]: https://i.ibb.co/dmfMDrD/image.png
And I filtered the unique mapping reads use command: `samtools view -q 20` , the reads with mapping quality lower than 20 were determined as multiple mapping reads. ...
written 11 months ago by
younglin113 • 40
Latest awards to younglin113
Popular Question
9 months ago,
created a question with more than 1,000 views.
For I got some diffculties when run rMATs
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1100 users visited in the last hour