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Forum: Illumina/Solexa Today, 06:47 AM
Replies: 2
Views: 26
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 Today, 04:19 AM
Replies: 1
Views: 72
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 Yesterday, 12:12 PM
Replies: 627
Views: 116,738
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: 65
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: 490
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: 278
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: 246
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: 210
Posted By GenoMax
Use TruSeq3-PE.fa file.

Use TruSeq3-PE.fa file.
Forum: Bioinformatics 04-12-2018, 03:38 AM
Replies: 627
Views: 116,738
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: 41,340
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: 1,257
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: 218
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: 512
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: 512
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: 627
Views: 116,738
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: 627
Views: 116,738
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: 305
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: 627
Views: 116,738
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....
Forum: Bioinformatics 04-07-2018, 06:17 AM
Replies: 627
Views: 116,738
Posted By GenoMax
BBMap is one of the aligners that uses the full...

BBMap is one of the aligners that uses the full header present in your fasta file when creating the index and passes it along to alignment file. If there are spaces in the header name they are...
Forum: Illumina/Solexa 04-05-2018, 07:51 AM
Replies: 1
Views: 307
Posted By GenoMax
Prevention of index hopping in Illumina tech

Illumina has announced free adapter blocking agents (https://www.illumina.com/products/by-type/accessory-products/free-adapter-blocking-reagent.html) which are supposed to help minimize index hopping.
Forum: Service Providers 04-04-2018, 01:18 PM
Replies: 7
Views: 391
Posted By GenoMax
Also: http://allseq.com/ Comparison shop but...

Also: http://allseq.com/ Comparison shop but compare the develerables list carefully before selecting a provider. Devil is always in the details.
Forum: Bioinformatics 04-02-2018, 04:28 AM
Replies: 2
Views: 299
Posted By GenoMax
1. If you are doing RNAseq then yes you would...

1. If you are doing RNAseq then yes you would sequence DNA that is derived from RNA. Unless you know beforehand the DNA being sequenced may be normal or mutated.
2. DESeq2 , edgeR and LIMMA are some...
Forum: Bioinformatics 03-29-2018, 04:39 PM
Replies: 3
Views: 729
Posted By GenoMax
Yes, because FastQC is a QC program. FastQC does...

Yes, because FastQC is a QC program. FastQC does not modify raw data. It is going to show you summary of the same Q-scores whether they come from the BAM or the fastq reads extracted from the BAM...
Forum: Bioinformatics 03-29-2018, 04:37 PM
Replies: 1
Views: 485
Posted By GenoMax
For reference cross-posted:...

For reference cross-posted: https://www.biostars.org/p/301685/#306693
Forum: Bioinformatics 03-29-2018, 08:02 AM
Replies: 627
Views: 116,738
Posted By GenoMax
I suggest that you create a ticket on BBMap SF...

I suggest that you create a ticket on BBMap SF site (https://sourceforge.net/p/bbmap/tickets/?source=navbar) since you have specifically identified a fix.
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