User: younglin113
younglin113 • 10
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Posts by younglin113
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... Thanks a lot. It's really helped my doubts. ...
written 4 weeks ago by
younglin113 • 10
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... 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
younglin113 • 10
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... 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 4 weeks ago by
younglin113 • 10
• updated
4 weeks ago by
finswimmer ♦ 11k
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... 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
younglin113 • 10
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... 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
younglin113 • 10
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... 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 4 weeks ago by
younglin113 • 10
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... 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
younglin113 • 10
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... 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
younglin113 • 10
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... 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
younglin113 • 10
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... 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
younglin113 • 10
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