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Search: Posts Made By: mgogol
Forum: Bioinformatics 01-28-2019, 07:03 AM
Replies: 10
Views: 4,186
Posted By mgogol
The cellranger pipeline generates gene level...

The cellranger pipeline generates gene level data, but you always have the fastq files if you want to go back and look at them another way. I'm not familiar with illumina ddseq.
Forum: Bioinformatics 01-24-2019, 01:15 PM
Replies: 10
Views: 4,186
Posted By mgogol
Great, I am glad you are making an effort to be...

Great, I am glad you are making an effort to be reproducible. I am clearly jumpy about this.
Forum: Bioinformatics 01-23-2019, 07:47 AM
Replies: 10
Views: 4,186
Posted By mgogol
Uh, I disagree that Seurat is for "one workflow"....

Uh, I disagree that Seurat is for "one workflow". It is quite flexible, with excellent documentation (https://satijalab.org/seurat/get_started.html) for a number of use cases that makes it pretty...
Forum: Bioinformatics 01-23-2019, 06:13 AM
Replies: 10
Views: 4,186
Posted By mgogol
Seurat and cellranger

cellranger is run on the raw data and produces data that you can read into R with Seurat for downstream analysis. It also does some processing of the data for instant visualization in the cellranger...
Forum: Bioinformatics 08-20-2015, 05:40 AM
Replies: 13
Views: 10,024
Posted By mgogol
Ah. The way I usually handle stuff like this is...

Ah. The way I usually handle stuff like this is just I have a text file listing all the files - in this case, in two columns. Then I have a perl script with a for loop going through each line in the...
Forum: Bioinformatics 08-07-2015, 05:48 AM
Replies: 5
Views: 1,001
Posted By mgogol
You don't need a Phd, but maybe a coursera course...

You don't need a Phd, but maybe a coursera course or two, or a few safari books on command line, R, and/or scripting languages could help.
Forum: Bioinformatics 06-24-2015, 06:48 AM
Replies: 13
Views: 10,024
Posted By mgogol
I bet you could do something snazzy with gnu...

I bet you could do something snazzy with gnu parallel.

http://figshare.com/articles/GNU_parallel_for_Bioinformatics_my_notebook/822138
Forum: Bioinformatics 10-03-2014, 12:17 PM
Replies: 3
Views: 2,332
Posted By mgogol
I've used trimmomatic with the adapters file that...

I've used trimmomatic with the adapters file that comes along with fastqc converted to a fasta file. Worked good. The As might be after it reads all the way through the adapter and isn't reading...
Forum: Bioinformatics 09-30-2014, 05:56 AM
Replies: 13
Views: 31,917
Posted By mgogol
Just add it as an argument. I wish this was...

Just add it as an argument. I wish this was better documented.

./fastx_trimmer -Q33 -t 30 -i <filename> -o <filename2>

I don't know if this one needs it as well?
fastq_to_fasta -Q33 -h -r -v...
Forum: Bioinformatics 08-08-2014, 10:36 AM
Replies: 7
Views: 2,178
Posted By mgogol
Oh, and for pure programming questions,...

Oh, and for pure programming questions, stackoverflow (http://stackoverflow.com/) is good. Search with [r] for R tagged questions, for example.
Forum: Bioinformatics 08-08-2014, 10:15 AM
Replies: 7
Views: 2,178
Posted By mgogol
I will just chime in on a few... 1)...

I will just chime in on a few...

1) Statistics is always a good bet.

2) Maybe this (https://www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401)?

6) Learn R! Bioconductor...
Forum: Bioinformatics 06-24-2014, 08:19 AM
Replies: 4
Views: 3,952
Posted By mgogol
I'm just starting out with NextSeq data by...

I'm just starting out with NextSeq data by installing bcl2fastq version 2. Haven't gotten as far as all that yet, but thanks for the heads up.
Forum: Bioinformatics 05-13-2014, 10:28 AM
Replies: 6
Views: 1,725
Posted By mgogol
Wow, worse than I thought it would be.

Wow, worse than I thought it would be.
Forum: Bioinformatics 05-06-2014, 05:53 AM
Replies: 6
Views: 1,725
Posted By mgogol
While I don't think my gender has limited my...

While I don't think my gender has limited my career prospects exactly (how would I know unless it was blatant), that's not to say I haven't been treated differently a few times because of my gender...
Forum: Bioinformatics 03-28-2014, 06:07 AM
Replies: 4
Views: 9,941
Posted By mgogol
Here's a few ideas: ...

Here's a few ideas:
https://groups.google.com/forum/#!topic/bedtools-discuss/gf0KeAJN2Cw

Also look into bamtools random
Forum: General 02-25-2014, 09:23 AM
Replies: 15
Views: 2,978
Posted By mgogol
You could do a lot with Galaxy + public data sets.

You could do a lot with Galaxy + public data sets.
Forum: Bioinformatics 01-15-2014, 09:00 AM
Replies: 7
Views: 1,523
Posted By mgogol
I don't think fastx can do that. You may try...

I don't think fastx can do that. You may try trimmomatic? Or some other options here:

http://www.biostars.org/p/53528/
Forum: General 01-10-2014, 07:17 AM
Replies: 9
Views: 6,623
Posted By mgogol
I do think institutions and society as a whole...

I do think institutions and society as a whole benefit from reasonable attempts to overcome the bias everyone has for hiring/promoting people similar to themselves. Or to rate male applicants as more...
Forum: General 01-08-2014, 05:53 AM
Replies: 9
Views: 6,623
Posted By mgogol
I think this is pretty unlikely. Maybe you...

I think this is pretty unlikely.

Maybe you should write a short story about it, though. If an organization was found to be enriched for a certain group, what would happen? Randomized firings?
Forum: Illumina/Solexa 12-05-2013, 05:54 AM
Replies: 18
Views: 5,632
Posted By mgogol
I find the kmer plots of fastqc useful for this....

I find the kmer plots of fastqc useful for this. If there are adapters at the end or something, you'll see the corresponding kmers coming up at the end. You can usually use this plus the contaminants...
Forum: Bioinformatics 11-14-2013, 07:18 AM
Replies: 10
Views: 9,978
Posted By mgogol
Thanks for improving on my hasty and incorrect...

Thanks for improving on my hasty and incorrect answer...
Forum: Bioinformatics 11-13-2013, 01:05 PM
Replies: 10
Views: 9,978
Posted By mgogol
I think you could do something by filtering on...

I think you could do something by filtering on the field XM:i:0 and XM:i:1 and XM:i:2 from the sam file.

Probably something like:

samtools view | cut whatever column it is | grep "XM:i:0" >...
Forum: Illumina/Solexa 11-06-2013, 08:12 AM
Replies: 18
Views: 8,084
Posted By mgogol
I think it was kind of shady of illumina to do...

I think it was kind of shady of illumina to do that. They should have been really clear when they announced it, at least.
Forum: Bioinformatics 11-05-2013, 06:18 AM
Replies: 2
Views: 2,185
Posted By mgogol
I have found that one job is enough for me the...

I have found that one job is enough for me the past 8 years... Your mileage may vary.

But you can always move. I would focus on finding an interesting job and then see if it's in a 'good enough'...
Forum: Bioinformatics 11-05-2013, 06:14 AM
Replies: 3
Views: 1,538
Posted By mgogol
I think FastQC and picard are sort of "enough."...

I think FastQC and picard are sort of "enough." But I know there are a few in R. Haven't used them.

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030619
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