User: Marius

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Marius20
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Posts by Marius

<prev • 11 results • page 1 of 2 • next >
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Comment: C: prepare pair-ended reads for peak calling
... Hi Ian, I have tried with the suggested parameter settings, but to no success. I have just accepted the fact that it does not produce the same results using BAMPE and BEDPE. I have contacted the developers/supporting team several times about this issue and other encountered on the way, but they did ...
written 2.0 years ago by Marius20
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Comment: C: prepare pair-ended reads for peak calling
... Hi Ian, sorry for the late reply. I will give it a try and come back with an answer in the following days. Meanwhile, I've discovered that some reads were mapped on different chromosomes (i.e., 1st read on chr1 for instance and the corresponding paired read on chr16). That, I guess it's `bowtie`. I ...
written 2.1 years ago by Marius20
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Comment: C: MACS2 produces different results using BAMPE and BEDPE
... I've sent an email to the support team earlier today, let's see if they answer.. thought it might be quicker via biostars as there are more ppl using MACS :] ...
written 2.1 years ago by Marius20
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Comment: C: MACS2 produces different results using BAMPE and BEDPE
... OK. I've performed a bunch of tests, but still no decent conclusion has been reached. If I use single-end reads as input in MACS2, from both `BAM` and `BED` formats I get identical resulting peak files. If I use pair-ended reads in `BAMPE` and `BEDPE` I get different resulting peak files using the s ...
written 2.1 years ago by Marius20
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Comment: C: prepare pair-ended reads for peak calling
... OK. I've performed a bunch of tests, but still no decent conclusion has been reached. If I use single-end reads as input in MACS2, from both `BAM` and `BED` formats I get identical resulting peak files. If I use pair-ended reads in `BAMPE` and `BEDPE` I get different resulting peak files using the s ...
written 2.1 years ago by Marius20
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Comment: C: MACS2 produces different results using BAMPE and BEDPE
... Hi James. Thanks for the reply. Looking at the xls files generated during the runs: For `BEDPE`: # fragment size is determined as 100 bps # total fragments in treatment: 29486407 # fragments after filtering in treatment: 19212868 # maximum duplicate fragments in treatment = 1 # ...
written 2.1 years ago by Marius20
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MACS2 produces different results using BAMPE and BEDPE
... Hi, I was performing some tests using the peak calling software MACS2 and I stumbled upon an issue: using pair-ended reads as input, I get different results using the same data set, but in `BAMPE` format and in `BEDPE` format. If I use a data set consisting of single-end reads, I do get the same re ...
macs2 chip-seq pair-ended written 2.1 years ago by Marius20
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Comment: C: prepare pair-ended reads for peak calling
... I am using both MACS and JAMM. Regarding pair-ended reads, MACS is smart enough to detect them. For [JAMM][1], I need BEDPE (or BED if it is formatted to contain all pair-end information in the first 3 columns..). I want to use JAMM also because supposedly it's able to identify narrower peaks than M ...
written 2.2 years ago by Marius20
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Comment: C: prepare pair-ended reads for peak calling
... Hi Ian, thanks for your reply. So, I actually have to create BEDPE files from the output of bowtie then. Isn't bowtie doing the 'right" thing with the pair-ended files while creating the BAM file and putting both mates as entries in the file? (BTW, I do not need to create a BED from the BEDPE) ...
written 2.2 years ago by Marius20
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Comment: C: prepare pair-ended reads for peak calling
... Hi Alexander. Thanks for the detailed and useful information. Reading through the `bedtools bamtobed` documentation I see indeed that they specify that if you want to use the `-bedpe` option, the BAM file should be sorted by read name. I was using `samtools sort -o ` without the `-n` option. I agree ...
written 2.2 years ago by Marius20

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