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Search took 0.06 seconds. Search: Posts Made By: GenoMax
Forum: RNA Sequencing Today, 03:39 AM
Replies: 1
Views: 98
Posted By GenoMax
Cross-posted: https://www.biostars.org/p/311462/

Cross-posted: https://www.biostars.org/p/311462/
Forum: Bioinformatics Yesterday, 05:26 AM
Replies: 1
Views: 65
Posted By GenoMax
Do you expect to see those poly-C and poly-T...

Do you expect to see those poly-C and poly-T stretches after ~106 position?
Forum: Illumina/Solexa 04-23-2018, 02:56 PM
Replies: 7
Views: 776
Posted By GenoMax
@nano85: I suggest that you actually calculate...

@nano85: I suggest that you actually calculate the insert sizes by using one of the methods noted by @Brian in post #2 here. (http://seqanswers.com/forums/showthread.php?t=73038)
Forum: Bioinformatics 04-23-2018, 03:48 AM
Replies: 632
Views: 117,690
Posted By GenoMax
Consider...

Consider http://seqanswers.com/forums/showthread.php?p=214346 (posts 204-206). BBMap does not seem to report ALL alignments in output file. @Brian may seen this and comment.
Forum: Illumina/Solexa 04-21-2018, 01:15 PM
Replies: 4
Views: 324
Posted By GenoMax
All new data should be phred+33. If you have data...

All new data should be phred+33. If you have data that is 5+ yr old then you have to worry about it being phred+33.
Forum: Illumina/Solexa 04-20-2018, 07:27 AM
Replies: 5
Views: 343
Posted By GenoMax
BBMap includes sequences of commonly used adapter...

BBMap includes sequences of commonly used adapter sequences (Illumina kits) in a file in BBMap software. Look for that file (adapters.fa) in "resources" directory of software distribution. You can...
Forum: Illumina/Solexa 04-19-2018, 05:00 PM
Replies: 5
Views: 343
Posted By GenoMax
You can't eyeball millions of reads. Use a...

You can't eyeball millions of reads. Use a program like bbduk (guide (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/)) and scan your files. If your data has no adapter...
Forum: Illumina/Solexa 04-19-2018, 06:47 AM
Replies: 2
Views: 111
Posted By GenoMax
There is no "best" aligner in a practical sense....

There is no "best" aligner in a practical sense. Most aligners will give you reasonable alignments that you should be able to use for expression analysis.

You want to make sure the aligner you...
Forum: Bioinformatics 04-19-2018, 04:19 AM
Replies: 3
Views: 185
Posted By GenoMax
Use mosdepth ...

Use mosdepth (https://github.com/brentp/mosdepth)and option --by 10000.

You can also use deepTools (https://deeptools.readthedocs.io/en/develop/)and option multiBamSummary bins.
Forum: Bioinformatics 04-18-2018, 12:12 PM
Replies: 632
Views: 117,690
Posted By GenoMax
We had a discussion...

We had a discussion (https://www.biostars.org/p/302867/) about what the x:y coordinates mean on Biostars.

Short take home from poster of that thread was:
Forum: Bioinformatics 04-17-2018, 11:07 AM
Replies: 1
Views: 114
Posted By GenoMax
For reference cross-posted:...

For reference cross-posted: https://www.biostars.org/p/309849/
Forum: Metagenomics 04-17-2018, 03:50 AM
Replies: 13
Views: 657
Posted By GenoMax
You need to use a scan/trim program (I recommend...

You need to use a scan/trim program (I recommend bbduk.sh from BBMap suite) to scan and trim your data. You can't depend on FastQC to identify dimer contamination. Here is bbduk guide...
Forum: Bioinformatics 04-13-2018, 08:10 AM
Replies: 1
Views: 328
Posted By GenoMax
Cross-posted: https://www.biostars.org/p/309209/

Cross-posted: https://www.biostars.org/p/309209/
Forum: Bioinformatics 04-12-2018, 03:43 AM
Replies: 1
Views: 273
Posted By GenoMax
I am reasonably sure that @Brian recommends...

I am reasonably sure that @Brian recommends merging first and then doing any trimming with bbduk.
Forum: Bioinformatics 04-12-2018, 03:40 AM
Replies: 1
Views: 231
Posted By GenoMax
Use TruSeq3-PE.fa file.

Use TruSeq3-PE.fa file.
Forum: Bioinformatics 04-12-2018, 03:38 AM
Replies: 632
Views: 117,690
Posted By GenoMax
Since you are using ambig=all you are going to...

Since you are using ambig=all you are going to get multi-mappers with their MAPQ being set to a small value (3). You could post filter your sam file or set ambig=toss (or ambig=random/best to get...
Forum: Bioinformatics 04-12-2018, 03:29 AM
Replies: 118
Views: 41,606
Posted By GenoMax
@chloe1005: It is possible that only 32% of your...

@chloe1005: It is possible that only 32% of your reads have inserts of a size that the reads can merge.

`trimq=30` is too severe a bar for trimming. If you have a reference genome then not doing...
Forum: RNA Sequencing 04-10-2018, 01:58 PM
Replies: 2
Views: 1,305
Posted By GenoMax
Even though the profile may be odd you should go...

Even though the profile may be odd you should go ahead and analyze the data to see what it looks like. Things may be fine.
Forum: Bioinformatics 04-10-2018, 01:53 PM
Replies: 1
Views: 230
Posted By GenoMax
It could be best to leave them in pieces while...

It could be best to leave them in pieces while you scan/trim/align them to allow brute-force parallelization. You can then merge the BAM files afterwards to generate a single one per sample.
...
Forum: Bioinformatics 04-10-2018, 01:50 PM
Replies: 7
Views: 554
Posted By GenoMax
NCBI/Ensembl want to make sure that there is one...

NCBI/Ensembl want to make sure that there is one authoritative source of clinically important transcripts since they want clinicians to use it.

I think we can use a single longest/most abundant...
Forum: Bioinformatics 04-10-2018, 05:10 AM
Replies: 7
Views: 554
Posted By GenoMax
Survey: help define Gencode and NCBI primary transcripts

Cross-posting this here since it will be of interest. Likely to remain open for 1 week.

-------------------------------------------

Ensembl and NCBI have been working to align the GENCODE and...
Forum: Bioinformatics 04-09-2018, 11:54 AM
Replies: 632
Views: 117,690
Posted By GenoMax
Try the following. Make sure you change /path/to/...

Try the following. Make sure you change /path/to/ to a real value on your computer.

java -ea -Xmx200m -cp /path/to/bbmap/current/ jgi.BBDukF in=reads.fq out=processed.fq
Forum: Bioinformatics 04-09-2018, 11:41 AM
Replies: 632
Views: 117,690
Posted By GenoMax
Are you including the entire fastq/fasta header...

Are you including the entire fastq/fasta header in your retrieval command?
Forum: Bioinformatics 04-08-2018, 01:57 PM
Replies: 2
Views: 311
Posted By GenoMax
Normally yes. I suggest that you use use...

Normally yes.

I suggest that you use use "repair.sh" from BBMap suite (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/repair-guide/) to re-pair the reads and remove singletons to a...
Forum: Bioinformatics 04-07-2018, 06:20 AM
Replies: 632
Views: 117,690
Posted By GenoMax
Index the genome independently by doing ...

Index the genome independently by doing

bbmap.sh ref=your_genome.fa

This will produce the index in the local directory. There will be a top level "ref" directory with several things in it....
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