User: magnuskerber

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magnuskerber10
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Posts by magnuskerber

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Comment: C: BWA-MEM read groups usage
... So, I did some digging on my raw reads and found 5 samples with the exact same read group naming. Since 5 samples are counting as 1 that explains the math of having "4 less samples" in the end. I know they came from different individuals because there is a table with the code names for each archive ...
written 4 months ago by magnuskerber10
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Comment: C: BWA-MEM read groups usage
... Yes, I thought about that. I ran mpileup before for a smaller set of those samples and this shrinking in the number of samples didn't happened. I'm using a bash script to prospect the read group of those samples, which I got from [this][1] topic. The part where I read the .fastq file to get read gro ...
written 4 months ago by magnuskerber10 • updated 4 months ago by genomax87k
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Comment: C: BWA-MEM read groups usage
... Hi, @genomax I added the read group successfully. But something odd happened, my samples number kinda downed. It was supposed to be 295 but after adding the read group my samples number downed to 291. The program starts now like: "[mpileup] 291 samples in 295 input files". ...
written 4 months ago by magnuskerber10
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Comment: A: BWA-MEM read groups usage
... Hi guys, thank you all for the answers. So I figured its better to add the read groups. I was reading some articles, including this one https://gatk.broadinstitute.org/hc/en-us/articles/360035890671?id=6472 but I didn`t get how does bwa-mem gets the information of lane/well/run of the samples and as ...
written 4 months ago by magnuskerber10
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BWA-MEM read groups usage
... So, I'm through the process of learning how to perform variant calling and doing some reading/tutorials, etc. I'm using the "BWA-MEM -> Samtools mpileup" strategy to do so. I figured that some people use bwa-mem with the -R option, which will add read group information to samples. But I did not ...
bwa-mem read groups alignment written 4 months ago by magnuskerber10
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Comment: C: Read length for metagenomics analysis
... Thank you all, your answers are helping me a lot. Yes, I will trimm my data always prior to analysis. I got the whole idea about the over-represented sequences, they're not necessarily a bad thing. My library was generated using the TruSeq kit from Illumina. I got the adapter sequences from their we ...
written 12 months ago by magnuskerber10
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Comment: C: Read length for metagenomics analysis
... Ok, thank you Mensur. I'll make a 70bp cut then. My data has a good quality so that is a good thing. I have a question about the overrepresented sequences removal, in my case they are around 50bp ( I know that by making a 70bp cut they'll be removed, but I'm asking for curiosity/knowledge). Here is ...
written 12 months ago by magnuskerber10
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Comment: C: Read length for metagenomics analysis
... Thanks h.mon, those are the images. So, I think I'll use a cutoff of 50bp. Is that ok based on the graphics? Or can I go a little bit higher, like 70-90? ...
written 12 months ago by magnuskerber10
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Comment: C: Read length for metagenomics analysis
... >Did you remove over-represented sequences as idenfied by FastQC? Why? You should remove adapters and other contaminants, but not necessarily over-represented sequences: these may represent the more abundant organism in your dataset, not contamination of any kind. That is interesting, do you us ...
written 12 months ago by magnuskerber10 • updated 12 months ago by h.mon30k
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Comment: C: Read length for metagenomics analysis
... **Do you consider useful a read of 1 nucleotide in length?** Hahah, of course no. About the highly conserved region the data is not only 16s, I'm not sure if you referred to that. **So you may perform a histogram of the read length distribution and take a decision based on that.** So, this is inter ...
written 12 months ago by magnuskerber10 • updated 12 months ago by h.mon30k

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