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Forum: Bioinformatics 06-28-2017, 10:51 AM
Replies: 6
Views: 1,486
Posted By deep639
I think trim_galore by default sets it quality...

I think trim_galore by default sets it quality trimming to 20, I have never tried to change the setting, usually a small percentage of reads are thrown out because of quality and adapter trimming.
Forum: Bioinformatics 06-28-2017, 09:48 AM
Replies: 6
Views: 1,486
Posted By deep639
Its always good to trim the adapters and do...

Its always good to trim the adapters and do quality trimming before running alignment. Quality trimming is usually done at q20 level. Programs like trim_galore can auto detect the adapter sequence...
Forum: Bioinformatics 03-24-2016, 04:05 PM
Replies: 0
Views: 2,043
Posted By deep639
MACS2 broad peak calling

Is there an explanation for what the broad-cutoff means for broad peak calling for MACS. In the documentation for MACS they say it is a q-value cutoff for a broad peak region? I ask because in my...
Forum: Bioinformatics 01-26-2016, 10:25 AM
Replies: 2
Views: 942
Posted By deep639
thanks for the link

thanks for the link
Forum: Bioinformatics 01-26-2016, 10:06 AM
Replies: 2
Views: 942
Posted By deep639
mm10 female mouse

I aligned samples from a female mouse to the mm10 genome, the samples were Illumina sequenced samples. After alignment, I found some reads aligned to chrY, are these reads false positive/artifacts. I...
Forum: Bioinformatics 10-02-2015, 10:44 AM
Replies: 2
Views: 1,077
Posted By deep639
Thanks, I let UCSC know about it.

Thanks, I let UCSC know about it.
Forum: Bioinformatics 10-01-2015, 04:29 PM
Replies: 2
Views: 1,077
Posted By deep639
UCSC and RefSeq Genes Track coordinate information

I had a question regarding two microRNA annotations. The two RNAs were Mir1195 and Mir5128. The reference genome was the mouse mm10 genome. They don't have the same coordinate information for UCSC...
Forum: General 01-29-2014, 09:13 AM
Replies: 1
Views: 864
Posted By deep639
Vcf files/Chipster

I used chipster (http://chipster.csc.fi/) to generate vcf files. I have 4 total vcf files. I am trying to view all 4 at the same time. I am annotating the vcf files for better comparison.
Forum: Bioinformatics 01-15-2014, 07:16 AM
Replies: 2
Views: 890
Posted By deep639
Thank you very much.

Thank you very much.
Forum: Bioinformatics 01-15-2014, 07:02 AM
Replies: 2
Views: 890
Posted By deep639
Mapping RNA seq reads

Hello, I am new to this forum. I am writing this thread because I wanted to know what would be the best way to go about mapping RNA seq reads that I have to my reference gneome (hg 19 genome). I have...
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