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Forum: Illumina/Solexa Today, 05:27 AM
Replies: 5
Views: 75
Posted By GenoMax
Sounds like you do your analysis in BaseSpace?...

Sounds like you do your analysis in BaseSpace? Was there a network failure of some kind?

Your best bet is to engage Illumina techsupport but someone else who uses BaseSpace may be able to help.
Forum: Illumina/Solexa 02-15-2018, 11:40 AM
Replies: 6
Views: 397
Posted By GenoMax
Following up @Phillip's suggestion, post this...

Following up @Phillip's suggestion, post this part from your ReadInfo.xml file for this run. It should look something like this

<Read Number="1" NumCycles="151" IsIndexedRead="N"/>
<Read...
Forum: Bioinformatics 02-15-2018, 06:52 AM
Replies: 1
Views: 162
Posted By GenoMax
Can you only try "-Xmx24052m threads=12" ? Don't...

Can you only try "-Xmx24052m threads=12" ? Don't use -Xms=.
Forum: Events / Conferences 02-14-2018, 04:22 AM
Replies: 2
Views: 268
Posted By GenoMax
Please check the registration URL/link since it...

Please check the registration URL/link since it is not working at moment.
Forum: Bioinformatics 02-13-2018, 04:37 AM
Replies: 1
Views: 340
Posted By GenoMax
Your best bet is to extract the accession numbers...

Your best bet is to extract the accession numbers of hits you are interested in from your blast output and then use the "blastbdbcmd" utility to retrieve the sequences from your blast database.
Forum: Bioinformatics 02-07-2018, 12:15 PM
Replies: 11
Views: 991
Posted By GenoMax
You should stop using TopHat for new projects....

You should stop using TopHat for new projects. Use BBMap, STAR, HISAT2 etc.
Forum: Bioinformatics 02-07-2018, 05:11 AM
Replies: 4
Views: 410
Posted By GenoMax
You can use bbduk.sh from BBMap suite...

You can use bbduk.sh from BBMap suite (http://seqanswers.com/forums/showthread.php?t=42776). Use "literal=CACACACACACA k=7" in addition to input output options.

Let me know if you need more help.
Forum: Bioinformatics 02-07-2018, 04:58 AM
Replies: 4
Views: 410
Posted By GenoMax
What is the data format, fastq or fasta?

What is the data format, fastq or fasta?
Forum: Bioinformatics 02-06-2018, 05:43 AM
Replies: 11
Views: 991
Posted By GenoMax
You could extract the unmapped reads from the...

You could extract the unmapped reads from the alignment you did (if you did include them in your alignment file) or redo the alignment and collect the unmapped reads in a separate file.

You could...
Forum: Bioinformatics 02-05-2018, 07:34 AM
Replies: 11
Views: 991
Posted By GenoMax
You say mRNA seq but had you done any ribosomal...

You say mRNA seq but had you done any ribosomal RNA depletion (e.g. https://www.illumina.com/products/by-type/molecular-biology-reagents/ribo-zero-rrna-removal-bacteria.html) on your samples? If not,...
Forum: Bioinformatics 02-01-2018, 10:43 AM
Replies: 4
Views: 416
Posted By GenoMax
Look into Geneious ...

Look into Geneious (https://www.geneious.com/pricing/c/), if you are ok going commercial.
Forum: Bioinformatics 02-01-2018, 09:35 AM
Replies: 4
Views: 416
Posted By GenoMax
Sounds like you are/were a power CLC user. When...

Sounds like you are/were a power CLC user. When you have used a program for a decade anything else you try is going to feel ... different. Following examples are more or less pure viewers.

IGB...
Forum: Introductions 02-01-2018, 06:27 AM
Replies: 2
Views: 267
Posted By GenoMax
Welcome to SA! You can use FastQC ...

Welcome to SA!

You can use FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)for assessment of quality of initial read data. This is pretty much the de facto program people use....
Forum: General 01-30-2018, 04:02 PM
Replies: 1
Views: 330
Posted By GenoMax
Can you tell us what you have learned as a part...

Can you tell us what you have learned as a part of this module? Do you know what the raw data looks like? What needs to be done with it in terms of QC/clean-up? Do you know what sequence alignment is...
Forum: Oxford Nanopore 01-30-2018, 09:57 AM
Replies: 3
Views: 319
Posted By GenoMax
RNAlater only stabilizes RNA, so it does not...

RNAlater only stabilizes RNA, so it does not degrade during transport/storage before the sample can be processed. There are many other things that need to happen before you get to sequencing....
Forum: Bioinformatics 01-25-2018, 09:38 AM
Replies: 2
Views: 347
Posted By GenoMax
For reference cross-posted to:...

For reference cross-posted to: https://www.biostars.org/p/295213/
Forum: Bioinformatics 01-25-2018, 04:54 AM
Replies: 14
Views: 741
Posted By GenoMax
While some of those fragments are flu virus they...

While some of those fragments are flu virus they are not of significant length. Especially if your aim is to put together reasonably complete genomes.

You will almost certainly need to do the...
Forum: Bioinformatics 01-24-2018, 06:41 AM
Replies: 206
Views: 44,783
Posted By GenoMax
I am not sure why BBMap is not reporting the two...

I am not sure why BBMap is not reporting the two sites in the output SAM. Perhaps that is by design.

Unfortunately @Brian has been missing from online forums for last couple of months. I pinged...
Forum: Illumina/Solexa 01-24-2018, 05:12 AM
Replies: 3
Views: 409
Posted By GenoMax
I have not seen any new ion around where I am...

I have not seen any new ion around where I am either. I assume you are thinking of getting the sequencing done from an external provider then?
Forum: Illumina/Solexa 01-24-2018, 04:59 AM
Replies: 3
Views: 409
Posted By GenoMax
Do you know if people are buying Ion in your part...

Do you know if people are buying Ion in your part of the world?
Forum: RNA Sequencing 01-24-2018, 04:49 AM
Replies: 3
Views: 322
Posted By GenoMax
Word of caution. Having a test of two "fail" (red...

Word of caution. Having a test of two "fail" (red X) in FastQC does not make your data automatically bad. If you have specific questions about anything post here with screenshots of FastQC data.
Forum: Bioinformatics 01-24-2018, 04:45 AM
Replies: 14
Views: 741
Posted By GenoMax
If you really have contig files then it signifies...

If you really have contig files then it signifies that you have assembled data i.e. sequence data that came from the sequencer has been processed and assembled. Is that the case? Assuming the...
Forum: RNA Sequencing 01-24-2018, 04:36 AM
Replies: 3
Views: 322
Posted By GenoMax
Read these posts...

Read these posts (https://sequencing.qcfail.com/software/fastqc/). Pay special attention to ones for duplicates, positional sequence bias at beginning of RNAseq reads.
Forum: Bioinformatics 01-22-2018, 07:41 AM
Replies: 4
Views: 461
Posted By GenoMax
Then you could use STAR once again in place of...

Then you could use STAR once again in place of "some_other_aligner" above.
Forum: Bioinformatics 01-22-2018, 07:12 AM
Replies: 4
Views: 461
Posted By GenoMax
You could use unix pipe (e.g. reformat.sh...

You could use unix pipe (e.g. reformat.sh in=your.sam out=stdout.fq | some_other_aligner commands sequence input from stdin ). reformat.sh comes from BBMap suite...
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