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Search: Posts Made By: GenoMax
Forum: Bioinformatics 01-17-2019, 10:00 AM
Replies: 9
Views: 16,580
Posted By GenoMax
Yes. As long as you only change the file name.

Yes. As long as you only change the file name.
Forum: Bioinformatics 01-17-2019, 08:22 AM
Replies: 1
Views: 112
Posted By GenoMax
NCBI uses ".fna" (for nucleotide) and ".faa" (for...

NCBI uses ".fna" (for nucleotide) and ".faa" (for protein) fasta format files. Changing the file extension to ".fa" will not affect results. HISAT2 should be able to use the ".fna" file as is. Is it...
Forum: Bioinformatics 01-17-2019, 08:21 AM
Replies: 9
Views: 16,580
Posted By GenoMax
No the results will not be affected since we are...

No the results will not be affected since we are not changing sequence/content of any data files. We are only renaming the file.
Forum: RNA Sequencing 01-11-2019, 11:41 AM
Replies: 1
Views: 292
Posted By GenoMax
You should contact 10x genomics tech support with...

You should contact 10x genomics tech support with this question. Post the info here when you hear from them so others can reference it in future.
Forum: Vendor Forum 01-09-2019, 03:10 PM
Replies: 2
Views: 304
Posted By GenoMax
Just curious which PacBio machine you are using...

Just curious which PacBio machine you are using for this service? Sequel?
Forum: Bioinformatics 01-09-2019, 03:09 PM
Replies: 2
Views: 251
Posted By GenoMax
#1 = Unless there is/are SNP's which are captured...

#1 = Unless there is/are SNP's which are captured by that particular read you would not be able to tell where the read came from. I assume the sequence of the gene is otherwise identical?
Forum: Bioinformatics 01-09-2019, 03:07 PM
Replies: 1
Views: 193
Posted By GenoMax
Cross-posted and answered on Biostars:...

Cross-posted and answered on Biostars: https://www.biostars.org/p/357359/#357497
Forum: Bioinformatics 01-06-2019, 06:25 PM
Replies: 314
Views: 91,997
Posted By GenoMax
@Seb: Brian does not seem to have time to respond...

@Seb: Brian does not seem to have time to respond to questions in this forum now a days but the different length of the adapters may have some bearing on this. Since the part you are looking for is...
Forum: Bioinformatics 01-04-2019, 12:33 PM
Replies: 3
Views: 463
Posted By GenoMax
You could also post this on Biostars.org using...

You could also post this on Biostars.org using "News" category.
Forum: Bioinformatics 12-20-2018, 05:05 AM
Replies: 314
Views: 91,997
Posted By GenoMax
@enma_ai: It is a bad idea to have spaces in your...

@enma_ai: It is a bad idea to have spaces in your file/directory names (even though your OS may allow it). I suggest the you change "NGS 10273-Raw" to "NGS_10273-Raw" and see if that fixes the error...
Forum: Illumina/Solexa 12-20-2018, 05:02 AM
Replies: 8
Views: 885
Posted By GenoMax
MiSeq is a sequencing champ as far as illumina...

MiSeq is a sequencing champ as far as illumina libraries are concerned. We look at results from MiSeq nano runs only qualitatively (rather than quantitatively) before the pools are transferred for...
Forum: 454 Pyrosequencing 12-18-2018, 08:51 AM
Replies: 3
Views: 846
Posted By GenoMax
Looks like they did. No obvious...

Looks like they did. No obvious announcements/comments from pundits anywhere either (google does not seem to bring anything up other than Qiagen's own site). Must be an application specific release.
Forum: General 12-11-2018, 08:35 AM
Replies: 1
Views: 373
Posted By GenoMax
In US, FDA has approved the following tests. All...

In US, FDA has approved the following tests. All other uses are in research settings.

https://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/ucm330711.htm...
Forum: Illumina/Solexa 12-10-2018, 04:01 AM
Replies: 8
Views: 1,412
Posted By GenoMax
I am glad things worked to your satisfaction....

I am glad things worked to your satisfaction. Thanks for providing a final update.
Forum: Bioinformatics 12-10-2018, 03:59 AM
Replies: 1
Views: 279
Posted By GenoMax
If samples are truly absent then you may not get...

If samples are truly absent then you may not get any reads assigned to them as long as your libraries are excellent quality and run has worked well.

That said if you allow errors during...
Forum: Bioinformatics 12-06-2018, 08:02 AM
Replies: 6
Views: 659
Posted By GenoMax
AFAIK, as long as you have enough memory...

AFAIK, as long as you have enough memory everything that works on a normal ubuntu machine should work on WSL as well (assuming you installed ubuntu).
Forum: Bioinformatics 12-06-2018, 04:55 AM
Replies: 3
Views: 299
Posted By GenoMax
You could also try to do this analysis in one...

You could also try to do this analysis in one step. Use bbsplit.sh from BBMap (http://seqanswers.com/forums/showthread.php?t=41288) with both genomes. Look for reads that map to both genomes. Those...
Forum: Bioinformatics 12-06-2018, 04:46 AM
Replies: 3
Views: 299
Posted By GenoMax
You can grab the header from your bam file by...

You can grab the header from your bam file by doing samtools view -H your.bam > header.txt That can then be added back to your filtered sam.
Forum: RNA Sequencing 12-03-2018, 03:56 PM
Replies: 1
Views: 497
Posted By GenoMax
At this point there is no reason to use TopHat...

At this point there is no reason to use TopHat for RNAseq analysis. There are current options like STAR, BBMap, HISAT2 which should be used.
Forum: Bioinformatics 11-30-2018, 06:57 AM
Replies: 1
Views: 401
Posted By GenoMax
You can use bbduk from BBMap suite...

You can use bbduk from BBMap suite (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) to remove adapter contamination. BBMap suite is pure java so it will work on windows...
Forum: Bioinformatics 11-30-2018, 06:54 AM
Replies: 1
Views: 505
Posted By GenoMax
I suggest that you use bbsplit.sh from BBMap...

I suggest that you use bbsplit.sh from BBMap suite (http://seqanswers.com/forums/showthread.php?t=41288) along with a copy of rDNA repeat (if available) for your organism to bin reads into rRNA and...
Forum: Illumina/Solexa 11-30-2018, 06:52 AM
Replies: 7
Views: 783
Posted By GenoMax
@misterc: Problem is a lot of times users (or...

@misterc: Problem is a lot of times users (or even the facility techs) may create samplesheets using IEM elsewhere and then bring those to the machine at the time of run-start. People may also want...
Forum: Illumina/Solexa 11-26-2018, 04:39 PM
Replies: 7
Views: 783
Posted By GenoMax
You should leave your MiSeq as is. Isolating...

You should leave your MiSeq as is. Isolating instrument computers from open internet with a strong firewall (preferably via a defined/separate VLAN) is the best option for securing instrument...
Forum: Bioinformatics 11-26-2018, 12:15 PM
Replies: 4
Views: 272
Posted By GenoMax
Use -r [<chr>:]<start>..<end> format in your...

Use -r [<chr>:]<start>..<end> format in your command.
Forum: Bioinformatics 11-26-2018, 12:05 PM
Replies: 4
Views: 272
Posted By GenoMax
You could potentially trim your gff file to...

You could potentially trim your gff file to contain just the chromosome you want.
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