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Search: Posts Made By: GenoMax
Forum: Bioinformatics 02-14-2020, 04:38 AM
Replies: 3
Views: 535
Posted By GenoMax
You are identifying changes w.r.t. a reference...

You are identifying changes w.r.t. a reference and then comparing those results to get the difference between your control and mutant results.
Forum: Bioinformatics 02-13-2020, 12:38 PM
Replies: 3
Views: 535
Posted By GenoMax
You need just step 1 from this tutorial ...

You need just step 1 from this tutorial (https://www.biostars.org/p/367960/) since you only want SNv.
Forum: Illumina/Solexa 02-06-2020, 07:25 AM
Replies: 2
Views: 236
Posted By GenoMax
While I don't have direct experience with MiniSeq...

While I don't have direct experience with MiniSeq it sounds like a problem with demultiplexing. Do you have an install of bcl2fastq available that you could use offline to do the demux again?
Forum: Sample Prep / Library Generation 02-06-2020, 05:12 AM
Replies: 21
Views: 5,398
Posted By GenoMax
Illumina did release a new version of RiboZero+...

Illumina did release a new version of RiboZero+ yesterday: https://www.illumina.com/products/by-type/accessory-products/ribo-zero-plus-rrna-depletion.html
Forum: Illumina/Solexa 02-04-2020, 04:28 PM
Replies: 3
Views: 282
Posted By GenoMax
Demultiplexing may fail, if your indexes are...

Demultiplexing may fail, if your indexes are non-standard and you provide standard indexes (but the run will not fail so don't worry). Edit the samplesheet and put the actual indexes you used. You...
Forum: Bioinformatics 02-04-2020, 07:00 AM
Replies: 2
Views: 211
Posted By GenoMax
Have you looked at this:...

Have you looked at this: http://seqanswers.com/forums/showthread.php?t=42552
Forum: General 02-03-2020, 05:24 PM
Replies: 1
Views: 296
Posted By GenoMax
Answered in this thread:...

Answered in this thread: http://seqanswers.com/forums/showthread.php?t=92819
Forum: Bioinformatics 02-03-2020, 05:23 PM
Replies: 4
Views: 338
Posted By GenoMax
There are databases e.g. SILVA...

There are databases e.g. SILVA (https://www.arb-silva.de/) that provide this information. NCBI (https://www.ncbi.nlm.nih.gov/refseq/targetedloci/16S_process/) also has a 16S microbial dataset.

As...
Forum: Bioinformatics 02-03-2020, 06:20 AM
Replies: 4
Views: 338
Posted By GenoMax
For analysis of 16S data you will want to use an...

For analysis of 16S data you will want to use an established pipeline such as Qiime (link (https://docs.qiime2.org/2019.10/)).
Forum: Bioinformatics 02-03-2020, 06:18 AM
Replies: 1
Views: 196
Posted By GenoMax
You could basically use any NGS aligner. bwa,...

You could basically use any NGS aligner. bwa, BBMap, bowie2 etc. You will need to use "samtools" to convert the resulting SAM alignment files into BAM (binary) format. You would want to do some basic...
Forum: Bioinformatics 01-27-2020, 05:10 AM
Replies: 2
Views: 382
Posted By GenoMax
Once you separate your sample pools based on...

Once you separate your sample pools based on Illumina demultiplexing you can then use a tool called sabre (https://github.com/najoshi/sabre)to demultiplex individual samples from the pool.
Forum: Bioinformatics 01-26-2020, 04:22 AM
Replies: 4
Views: 665
Posted By GenoMax
If you feel your files have become corrupt you...

If you feel your files have become corrupt you can use "validateFiles" utility (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/validateFiles) from Jim Kent to verify the files. Add execute...
Forum: Bioinformatics 01-24-2020, 02:17 PM
Replies: 4
Views: 665
Posted By GenoMax
How are you running the fastqc program? You re...

How are you running the fastqc program? You re running out of memory.

If you are using the bat file on windows then be sure to edit that and increase the value for memory allocation by changing...
Forum: Bioinformatics 01-24-2020, 04:11 AM
Replies: 3
Views: 562
Posted By GenoMax
How much memory are you assigning to this job?...

How much memory are you assigning to this job? Have these reads been scanned/trimmed before splitting?

Have you also looked at the output of these reports?

scafstats=<file> Write...
Forum: Bioinformatics 01-23-2020, 07:46 AM
Replies: 3
Views: 562
Posted By GenoMax
Have you checked the options about what to do if...

Have you checked the options about what to do if reads are multi-mapping to more than one reference? I am going to hazard a guess that you just have some.
Forum: Bioinformatics 01-21-2020, 10:11 AM
Replies: 1
Views: 255
Posted By GenoMax
Have you checked to make sure that your input...

Have you checked to make sure that your input sequence files are in sync as far as R1/R2 go. You can use `repair.sh` from BBMap suite to bring them in sync if they are not (e.g. if mates are missing...
Forum: Bioinformatics 01-17-2020, 05:23 AM
Replies: 2
Views: 1,122
Posted By GenoMax
The file extension indicates gzip compression....

The file extension indicates gzip compression. You should be able to use "gunzip" program to uncompress the file. On windows you may want to use a program such as 7-zip to do this conversion.
Forum: Bioinformatics 01-05-2020, 05:01 AM
Replies: 33
Views: 13,653
Posted By GenoMax
@uloeber: @Brian described the method of masking...

@uloeber: @Brian described the method of masking in first post of this thread. It uses "bbmask.sh" which is a component of BBMap suite. Take a look at in-line help for bbmask.sh to get an idea of...
Forum: Bioinformatics 12-31-2019, 03:45 PM
Replies: 2
Views: 1,183
Posted By GenoMax
You can access the normalized counts:...

You can access the normalized counts: https://support.bioconductor.org/p/66067/ Take a look at DESeq2 vignette (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html) for...
Forum: Bioinformatics 12-20-2019, 09:11 AM
Replies: 7
Views: 4,214
Posted By GenoMax
@Luckyboy7: Use deML package to demux your data....

@Luckyboy7: Use deML package to demux your data. More info here (https://github.com/grenaud/deML).
Forum: Bioinformatics 12-13-2019, 03:58 AM
Replies: 2
Views: 818
Posted By GenoMax
Rather than doing the filtering you should...

Rather than doing the filtering you should consider normalizing your data. For this BBMap has another program called bbnorm.sh. You can find a guide here...
Forum: Bioinformatics 12-12-2019, 09:36 AM
Replies: 678
Views: 184,033
Posted By GenoMax
@Robinsleith: I suggest that you post this as a...

@Robinsleith: I suggest that you post this as a ticket (https://sourceforge.net/p/bbmap/tickets/)on BBMap SF page. Brian no longer visits SeqAnswers regularly. He would be the only person who can...
Forum: RNA Sequencing 11-21-2019, 04:31 AM
Replies: 4
Views: 950
Posted By GenoMax
OP says these are from iSeq.

OP says these are from iSeq.
Forum: Bioinformatics 11-21-2019, 04:28 AM
Replies: 4
Views: 663
Posted By GenoMax
@Kapara sometimes reality does not follow what is...

@Kapara sometimes reality does not follow what is written in the paper. Journals don't always enforce these claim submissions so it would be best to email the authors and confirm.
Forum: Bioinformatics 11-20-2019, 04:48 AM
Replies: 4
Views: 663
Posted By GenoMax
People may not always submit the corresponding...

People may not always submit the corresponding assemblies to NCBI. You could email the authors and ask.
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