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Forum: Bioinformatics 02-24-2017, 03:11 PM
Replies: 13
Views: 1,982
Posted By bloosnail
Here is a link to the screen output from the...

Here is a link to the screen output from the command that I posted earlier: https://drive.google.com/open?id=0B_kpdLuthDGCY0ZCQ3dQei1aUFU

Also, the number of input reads at the bottom should be...
Forum: Bioinformatics 02-24-2017, 10:54 AM
Replies: 13
Views: 1,982
Posted By bloosnail
Thank you for your thorough and quick response...

Thank you for your thorough and quick response Brian. I have tried Seal out and it seems to be giving the correct output -- same number of reads but the multi-mapped reads have different IDs on them....
Forum: Bioinformatics 02-23-2017, 05:00 PM
Replies: 13
Views: 1,982
Posted By bloosnail
Hi Brian, I am looking more closely at the...

Hi Brian,

I am looking more closely at the output from BBDuk and I think there may be a problem. It appears that whenever a read has multiple matches, the name of the barcode that is aligned to...
Forum: Bioinformatics 02-19-2017, 12:09 PM
Replies: 13
Views: 1,982
Posted By bloosnail
@Brian, I am currently running BBDuk and it seems...

@Brian, I am currently running BBDuk and it seems to be working well. Thank you for your suggestion. I am wondering if there is reasonable increase in time if more cores are used -- from the...
Forum: Bioinformatics 02-17-2017, 11:34 AM
Replies: 13
Views: 1,982
Posted By bloosnail
Hi Brian, Thank you for your response, this...

Hi Brian,

Thank you for your response, this seems to be useful for our purposes. I am wondering if BBDuk has some functionality to output the actual sequence in the .fa that each read aligned to,...
Forum: Bioinformatics 02-16-2017, 05:36 PM
Replies: 13
Views: 1,982
Posted By bloosnail
Good way to align very, very short reads?

We have single-cell transcriptomic reads, where each read has a barcode associated with it which designates which cell it came from. From the default pipeline (a company called 10X Genomics), about...
Forum: Metagenomics 12-10-2016, 09:59 PM
Replies: 5
Views: 2,106
Posted By bloosnail
Thank you for the quick response. The idea of...

Thank you for the quick response. The idea of assembling the reads into contigs before alignment makes sense, I will let me supervisor know. Do you know of good software to do this? I have tried...
Forum: Metagenomics 12-10-2016, 12:05 PM
Replies: 5
Views: 2,106
Posted By bloosnail
Minimum amount of data needed for reliable results?

We are trying to do analysis for whole genome metagenomic data taken from the surface of the eye. Each sample has millions of reads generated, but of those reads at most only 1-2% are bacterial...
Forum: Metagenomics 06-15-2016, 10:49 AM
Replies: 11
Views: 1,818
Posted By bloosnail
Oh, yes I was referring to the actual number. So...

Oh, yes I was referring to the actual number. So getting the number must be done with the real bacteria before sequencing?
Forum: Metagenomics 06-15-2016, 09:47 AM
Replies: 11
Views: 1,818
Posted By bloosnail
We only looked at bacterial DNA so far, if you...

We only looked at bacterial DNA so far, if you have reference genomes for the viruses in question I can try aligning back to them and let you know. Thank you for your suggestion about the...
Forum: Metagenomics 06-14-2016, 11:06 AM
Replies: 11
Views: 1,818
Posted By bloosnail
I agree with you that the single-endedness may be...

I agree with you that the single-endedness may be because of the high error rates. For now I suppose I will keep single reads even if their pair does not pass quality control since it seems much of...
Forum: Metagenomics 06-14-2016, 10:42 AM
Replies: 11
Views: 1,818
Posted By bloosnail
@fanli, I was unaware that the first read in a...

@fanli, I was unaware that the first read in a pair generally has better quality, thank you for pointing that out. I have run FastQC and it appears that in general the first reads have much better...
Forum: Metagenomics 06-13-2016, 10:37 PM
Replies: 11
Views: 1,818
Posted By bloosnail
Question about whole genome metagenomics for the microbiome?

Hello,

Thank you for taking the time to read my post. I currently have whole genome metagenomic data taken from the eye, with the reads being a mix of human DNA and a number of different...
Forum: Bioinformatics 07-25-2015, 12:38 PM
Replies: 6
Views: 513
Posted By bloosnail
Great, thanks a lot! Very helpful.

Great, thanks a lot! Very helpful.
Forum: Bioinformatics 07-24-2015, 11:20 AM
Replies: 6
Views: 513
Posted By bloosnail
Thank you for your informative response. What you...

Thank you for your informative response. What you said is making a lot of sense, and it seems to be a good choice to proceed with the original plan of just using the longer read platform.

I am...
Forum: Bioinformatics 07-24-2015, 10:09 AM
Replies: 6
Views: 513
Posted By bloosnail
Brian, are you saying to trim the 75bp reads down...

Brian, are you saying to trim the 75bp reads down to 50bp and then compare these trimmed reads to the ones that were originally 50bp?

To clarify, the goal at this step is not to use both platforms...
Forum: Bioinformatics 07-24-2015, 09:57 AM
Replies: 6
Views: 513
Posted By bloosnail
Comparing read lengths of duplicates

Hi All,

I can normally find answers to questions via searching but I couldn't this time so I made an account. I am wondering how to compare samples with different read lengths -- we have 5 75bp...
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