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Forum: RNA Sequencing Yesterday, 02:13 PM
Replies: 2
Views: 96
Posted By GenoMax
Open any web browser you like and then navigate...

Open any web browser you like and then navigate to that html file and open it. There is nothing special about firefox.
Forum: Bioinformatics Yesterday, 06:50 AM
Replies: 31
Views: 18,110
Posted By GenoMax
You could use `repair.sh` to separate the...

You could use `repair.sh` to separate the singletons out afterwards.
Forum: Bioinformatics 02-13-2019, 04:34 PM
Replies: 1
Views: 122
Posted By GenoMax
Can you try running by specifying the memory by...

Can you try running by specifying the memory by adding "-Xmx4g" to your command?
Forum: RNA Sequencing 02-13-2019, 04:29 PM
Replies: 4
Views: 145
Posted By GenoMax
Correct. That executable is likely in the "bin"...

Correct. That executable is likely in the "bin" directory that you see above. So you could have run it by saying $ bin/fastq-dump --outdir raw/ --split-3 --gzip SRR359063
Forum: RNA Sequencing 02-13-2019, 12:45 PM
Replies: 4
Views: 145
Posted By GenoMax
The directory you have the program "fastq-dump"...

The directory you have the program "fastq-dump" is likely not in your $PATH ( a set of directories that are automatically searched when you try to run something). You could try ./fastq-dump if the...
Forum: Bioinformatics 02-12-2019, 12:40 PM
Replies: 8
Views: 190
Posted By GenoMax
I am wondering if the error you are seeing is a...

I am wondering if the error you are seeing is a red herring. How much memory are you allocating to this job on the cluster (bbsplit can need a lot of memory depending on size of the reference...
Forum: Bioinformatics 02-12-2019, 10:09 AM
Replies: 8
Views: 190
Posted By GenoMax
Can you validate your fastq files to make sure...

Can you validate your fastq files to make sure there are no errors in the file?

Use validateFiles (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/validateFiles)from Kent Utilities (UCSC)....
Forum: Bioinformatics 02-11-2019, 03:20 PM
Replies: 8
Views: 190
Posted By GenoMax
BBSplit will take fastq reads and bin them. Let...

BBSplit will take fastq reads and bin them. Let me know how that works.

You can convert the merged fastq reads afterwards with reformat.sh in=merged.fq.gz out=merged.fa No paste/cut/sed needed...
Forum: Bioinformatics 02-11-2019, 12:26 PM
Replies: 8
Views: 190
Posted By GenoMax
Do you get an error right away or does the...

Do you get an error right away or does the program run for some time?

Are these bbmerged reads? Wonder if you should try to do the binning with original fastq data. Is that a possibility?
Forum: Bioinformatics 02-11-2019, 12:23 PM
Replies: 1
Views: 160
Posted By GenoMax
Are you sure about tablet not being able to open...

Are you sure about tablet not being able to open more than one alignment?

In any case IGV will allow you to open multiple files (aligned to same genome). You will need to make sure you have enough...
Forum: Bioinformatics 02-10-2019, 04:59 PM
Replies: 1
Views: 133
Posted By GenoMax
You could use "reformat" from BBMap suite. It...

You could use "reformat" from BBMap suite. It will work in Windows as long as you have Java 1.8. Look at the sampling parameters to select an appropriate one.
Forum: Bioinformatics 02-07-2019, 04:46 AM
Replies: 320
Views: 94,924
Posted By GenoMax
We are making progress! How much memory do...

We are making progress!

How much memory do you have on this Mac? I suggest using 85% of the maximum memory you have available with BBTools. You also need to specify "in1= and out1=" to go with...
Forum: Bioinformatics 02-06-2019, 09:31 AM
Replies: 320
Views: 94,924
Posted By GenoMax
On a Mac I tested this on nothing else was needed...

On a Mac I tested this on nothing else was needed to be done. What happens if you just run "bbmap.sh". Does that produce "in-line" bbmap help output?

Which Java version are you using on your Mac?
Forum: Bioinformatics 02-06-2019, 05:52 AM
Replies: 320
Views: 94,924
Posted By GenoMax
I am not sure why you are having this problem....

I am not sure why you are having this problem. All you should need to do is download BBMap software on your mac. Unarchive the tar-zipped file and then extend your path to include the "bbmap"...
Forum: Sample Prep / Library Generation 02-01-2019, 04:00 AM
Replies: 8
Views: 1,278
Posted By GenoMax
Just to be sure do you mean 70-90% of final reads...

Just to be sure do you mean 70-90% of final reads are still rRNA? @MU_Core and @evan_seq24?
Forum: Bioinformatics 01-31-2019, 06:34 AM
Replies: 2
Views: 240
Posted By GenoMax
Are you doing this on windows? You have not moved...

Are you doing this on windows? You have not moved any of the contents of BBMap software folder after you downloaded it?
Forum: Bioinformatics 01-28-2019, 04:53 AM
Replies: 1
Views: 326
Posted By GenoMax
You can take a look at this WikiBoooks entry on...

You can take a look at this WikiBoooks entry on NGS data genome assembly (https://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)/De_novo_assembly)to get an indea of what would be involved.
...
Forum: Bioinformatics 01-27-2019, 05:34 AM
Replies: 50
Views: 24,404
Posted By GenoMax
@Maya: Can you explicitly add -Xmx128g (is that...

@Maya: Can you explicitly add -Xmx128g (is that what you are asking for) threads=24 in your bbnorm.sh command?

I also don't understand this part: in=$fastq_DATA/petrosia_SE.fastq out=...
Forum: Bioinformatics 01-25-2019, 04:41 AM
Replies: 663
Views: 147,258
Posted By GenoMax
I see that you are using samtools module as well....

I see that you are using samtools module as well. With that you can directly write BAM files no need to use SAM.

So let us try a modified command line and see what happens (I am going to assume...
Forum: Bioinformatics 01-24-2019, 12:46 PM
Replies: 663
Views: 147,258
Posted By GenoMax
Have you verified that the $i variable is...

Have you verified that the $i variable is expanding correctly?

If you have multiple files to align you should first create an index by doing

bbmap.sh...
Forum: Bioinformatics 01-17-2019, 10:00 AM
Replies: 9
Views: 17,460
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: 230
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: 17,460
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: 450
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: 421
Posted By GenoMax
Just curious which PacBio machine you are using...

Just curious which PacBio machine you are using for this service? Sequel?
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