User: younglin113

gravatar for younglin113
younglin11310
Reputation:
10
Status:
New User
Location:
Last seen:
8 hours ago
Joined:
1 year ago
Email:
y**********@gmail.com

Posts by younglin113

<prev • 24 results • page 1 of 3 • next >
0
votes
2
answers
112
views
2
answers
Comment: C: The confused result of samtools sort
... Thanks a lot. It's really helped my doubts. ...
written 4 weeks ago by younglin11310
0
votes
2
answers
112
views
2
answers
Comment: C: The confused result of samtools sort
... 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 4 weeks ago by younglin11310
2
votes
2
answers
112
views
2
answers
The confused result of samtools sort
... 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 ...
software error alignment rna-seq written 4 weeks ago by younglin11310 • updated 4 weeks ago by finswimmer11k
0
votes
0
answers
134
views
0
answers
Comment: C: About the ERCC spike-in sequence reads quantification
... 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 4 weeks ago by younglin11310
0
votes
0
answers
134
views
0
answers
Comment: C: About the ERCC spike-in sequence reads quantification
... 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 4 weeks ago by younglin11310
0
votes
0
answers
134
views
0
answers
About the ERCC spike-in sequence reads quantification
... 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 ...
genome gene next-gen rna-seq sequencing written 4 weeks ago by younglin11310
0
votes
1
answer
247
views
1
answers
Comment: C: low unique mapping ratio of RNA-seq data
... 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 6 weeks ago by younglin11310
0
votes
1
answer
247
views
1
answers
Comment: C: low unique mapping ratio of RNA-seq data
... 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 6 weeks ago by younglin11310
0
votes
1
answer
247
views
1
answers
Comment: C: low unique mapping ratio of RNA-seq data
... Actually, many papers show that they will use unique mapping reads for downstream analysis. And once I saw a writer said we could use the threshold of Q>20 to filter the unique mapping reads. That how my results came. ...
written 6 weeks ago by younglin11310
0
votes
1
answer
247
views
1
answers
Comment: C: low unique mapping ratio of RNA-seq data
... Thanks a lot for your help. I did define the fraction of rRNA by mapping all clean reads to rRNA sequences. ...
written 6 weeks ago by younglin11310

Latest awards to younglin113

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1685 users visited in the last hour