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Forum: RNA Sequencing 03-26-2020, 04:24 AM
Replies: 2
Views: 83
Posted By GenoMax
Rather then indeterminate, N signifies that a...

Rather then indeterminate, N signifies that a reliable base call is not possible at that location.

N's are also included to indicate locations where current sequencing technologies are unable to...
Forum: Bioinformatics 03-19-2020, 06:05 PM
Replies: 1
Views: 290
Posted By GenoMax
Listen to your IT recommendations. It is one...

Listen to your IT recommendations. It is one thing to have cores but if you don't have storage infrastructure to support the I/O needs then that will always be the bottleneck. When you run these...
Forum: RNA Sequencing 03-16-2020, 07:30 AM
Replies: 7
Views: 669
Posted By GenoMax
You should scan and trim the data before aligning...

You should scan and trim the data before aligning if there are substantial poly-G tails present.

You can find the sequence of human rDNA repeat here (http://www.ncbi.nlm.nih.gov/nuccore/U13369),...
Forum: Bioinformatics 03-10-2020, 04:13 AM
Replies: 243
Views: 95,489
Posted By GenoMax
@roselaw27: You can use `-F` option with...

@roselaw27: You can use `-F` option with fastq-dump to try and recreate fastq headers in original illumina format.
Forum: Bioinformatics 03-02-2020, 01:53 AM
Replies: 1
Views: 543
Posted By GenoMax
Cross-posted and answered on Biostars:...

Cross-posted and answered on Biostars: https://www.biostars.org/p/424091/
Forum: Illumina/Solexa 02-27-2020, 04:10 AM
Replies: 4
Views: 1,064
Posted By GenoMax
Since these systems have not been released as yet...

Since these systems have not been released as yet it is not surprising that the information is not yet available. Only thing publicly available seems to be this spec sheet...
Forum: Bioinformatics 02-22-2020, 03:26 AM
Replies: 1
Views: 661
Posted By GenoMax
Cross-posted on biostars:...

Cross-posted on biostars: https://www.biostars.org/p/423541/

I will keep answering there.
Forum: Bioinformatics 02-14-2020, 03:38 AM
Replies: 3
Views: 823
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, 11:38 AM
Replies: 3
Views: 823
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, 06:25 AM
Replies: 2
Views: 528
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, 04:12 AM
Replies: 21
Views: 5,963
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, 03:28 PM
Replies: 5
Views: 690
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, 06:00 AM
Replies: 2
Views: 420
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, 04:24 PM
Replies: 1
Views: 729
Posted By GenoMax
Answered in this thread:...

Answered in this thread: http://seqanswers.com/forums/showthread.php?t=92819
Forum: Bioinformatics 02-03-2020, 04:23 PM
Replies: 4
Views: 530
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, 05:20 AM
Replies: 4
Views: 530
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, 05:18 AM
Replies: 1
Views: 370
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, 04:10 AM
Replies: 2
Views: 491
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, 03:22 AM
Replies: 4
Views: 791
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, 01:17 PM
Replies: 4
Views: 791
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, 03:11 AM
Replies: 3
Views: 688
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, 06:46 AM
Replies: 3
Views: 688
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, 09:11 AM
Replies: 1
Views: 321
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, 04:23 AM
Replies: 2
Views: 1,301
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, 04:01 AM
Replies: 33
Views: 14,239
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...
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