User: heir_of_isildur88

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Posts by heir_of_isildur88

<prev • 22 results • page 1 of 3 • next >
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Answer: A: Viewer which shows F & R strand as top & bottom peaks from the sequence line
... Thank you for your replies. I will give it a shot by converting it to bedgraph and view it on IGV as I am using a custom virus genome which is not available in UCSC Genome Browser. Thanks very much again! ...
written 3 days ago by heir_of_isildur8810
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Viewer which shows F & R strand as top & bottom peaks from the sequence line
... Hi all, I found this nice figure which shows the reads of the forward and reverse strand as peaks in the upward and downward direction respectively from the sequence line. Figure link is https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020079/figure/F1/ and I am referring to the RNA-Seq data in the ...
alignment written 4 days ago by heir_of_isildur8810
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How to demultiplex dual-index NextSeq data for random index 2?
... Hi all, I have a question here and I could not find any sufficient information about this. Hope someone is able to help. I have a set of NextSeq data sequenced pair-end, dual-indexed whereby the index2 is a 8bp random index. The cycle run is 76, 8, 8 and 76 for R1, I1, I2, R2 respectively. I wan ...
next-gen sequencing written 6 weeks ago by heir_of_isildur8810
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Comment: C: Counting paired-end sequencing mapped reads
... OK, that clarifies a lot of things. But then, what about when the "properly paired" number is odd? It's not always an even number, right? For example, R1 can map to 2 different R2 fragments, how do you count those? I am quite new to sequencing, so I would like to know what is the general consensus ...
written 9 months ago by heir_of_isildur8810
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Comment: C: Counting paired-end sequencing mapped reads
... Thanks Pierre for the reply. But I still don't quite understand. I attached a picture to make my query clearer. image url In the picture, the flagstat showed 6 reads; 3 from R1 & 3 from R2. I understand that. But if you view the sam file in a genomic viewer like IGV, the first image appears. ...
written 9 months ago by heir_of_isildur8810
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Counting paired-end sequencing mapped reads
... Hi all, I have a very basic question here. With a paired-end sequencing, how do we count the number of mapped reads? I did a flagstat on my file which I have already filtered with the flags 83 & 163 for mapped proper and properly paired. The flagstat results are as below: 69640 + 0 in total ...
sequencing written 9 months ago by heir_of_isildur8810 • updated 9 months ago by Pierre Lindenbaum104k
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Comment: C: How to analyze CAGE-Seq data?
... Thank you for your suggestion. I will try it out and see if it works. ...
written 10 months ago by heir_of_isildur8810
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Comment: C: How to analyze CAGE-Seq data?
... Thank you very much! I will try it out and see if it work out for my data. ...
written 10 months ago by heir_of_isildur8810
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Comment: C: How to analyze CAGE-Seq data?
... How do you transform aligned reads to TSS positions? Thank you very much for your references. ...
written 10 months ago by heir_of_isildur8810
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Comment: C: How to analyze CAGE-Seq data?
... Here's the reads processing before mapping... 1. Index identification of samples - using custom perl file **read_skipper.pl R1_step1.fq CAC** 2. Trim away the index **fastx_trimmer -f 4 -i R1_step1.fq -o R1_trimmed.fq -Q33** 3. Using perl file to remove reads with Q<20 **perl ../IndexQualit ...
written 10 months ago by heir_of_isildur8810

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