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Search: Posts Made By: GenoMax
Forum: Bioinformatics Today, 04:48 AM
Replies: 1
Views: 85
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.
Forum: Sample Prep / Library Generation 11-12-2019, 04:59 AM
Replies: 16
Views: 4,094
Posted By GenoMax
Illumina is going to re-introduce ribozero...

Illumina is going to re-introduce ribozero equivalent kits in 2020.
Forum: Bioinformatics 11-08-2019, 08:41 AM
Replies: 1
Views: 245
Posted By GenoMax
Cross-posted and answered on biostars:...

Cross-posted and answered on biostars: https://www.biostars.org/p/407019/
Forum: Bioinformatics 11-08-2019, 06:32 AM
Replies: 2
Views: 289
Posted By GenoMax
You could add a "restrictleft=N" N=certain number...

You could add a "restrictleft=N" N=certain number of bases to look only in that area. Also adding "minlength=N" will exclude small reads like the first example. Also try setting k to something...
Forum: Illumina/Solexa 11-06-2019, 10:22 AM
Replies: 18
Views: 660
Posted By GenoMax
That does not jive with read numbers. Are you...

That does not jive with read numbers. Are you referring to 23M total reads (R1+R2) or passing clusters?

That cluster density if not very high to get to 20+M clusters.
Forum: Illumina/Solexa 11-01-2019, 10:16 AM
Replies: 3
Views: 419
Posted By GenoMax
I assume you have eliminated a faulty UPS as a...

I assume you have eliminated a faulty UPS as a possible cause? If your sequencer is under a maintenance contract you should contact Illumina tech support ASAP.

Never seen a sequencer just die...
Forum: Illumina/Solexa 11-01-2019, 09:44 AM
Replies: 3
Views: 419
Posted By GenoMax
As in the sequencer just died while the power was...

As in the sequencer just died while the power was still on in building? Do you not use UPS's on your sequencers to filter out power anomalies?
Forum: Illumina/Solexa 10-29-2019, 04:14 AM
Replies: 7
Views: 570
Posted By GenoMax
You may not have any adapters present if your...

You may not have any adapters present if your inserts were of a good size and there was no read-through.

BBMap suite provides an adapters.fa file in the "resources" directory. You can use it to...
Forum: Illumina/Solexa 10-23-2019, 06:03 AM
Replies: 6
Views: 382
Posted By GenoMax
Smaller inserts do tend to cluster more...

Smaller inserts do tend to cluster more efficiently on flowcells. Can you tell us what the cluster density was? You may need to deliberately underload the run to keep cluster density in check and/or...
Forum: Illumina/Solexa 10-23-2019, 05:52 AM
Replies: 6
Views: 382
Posted By GenoMax
When you say 20 bp span does that mean you have...

When you say 20 bp span does that mean you have just a 20 bp insert?
Forum: Illumina/Solexa 10-23-2019, 05:42 AM
Replies: 7
Views: 570
Posted By GenoMax
Do a google search with "QIAseq FX DNA". Second...

Do a google search with "QIAseq FX DNA". Second link in that search should be a PDF file with title "QIAGENŽ QIAseq FX DNA Library Kit Handbook". Check Appendix C in that file for sequences.
...
Forum: Illumina/Solexa 10-23-2019, 05:24 AM
Replies: 2
Views: 686
Posted By GenoMax
Yes it is possible to do 384 (and many more if...

Yes it is possible to do 384 (and many more if you do custom designs).



See this page (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-dna-flex.html).
Forum: RNA Sequencing 10-10-2019, 06:14 AM
Replies: 3
Views: 360
Posted By GenoMax
No need to delete. If someone finds this thread...

No need to delete. If someone finds this thread by search they will know where to get the answer.
Forum: RNA Sequencing 10-10-2019, 05:27 AM
Replies: 3
Views: 360
Posted By GenoMax
Cross-posted (and has a possible answer):...

Cross-posted (and has a possible answer): https://www.biostars.org/p/402237/
Forum: Bioinformatics 09-26-2019, 04:18 AM
Replies: 35
Views: 23,603
Posted By GenoMax
Did you move any of the bbmap folder contents...

Did you move any of the bbmap folder contents after you downloaded and uncompressed bbmap code?

Make sure the top level directory with BBMap is in your $PATH. Something like export...
Forum: Illumina/Solexa 09-21-2019, 07:24 AM
Replies: 2
Views: 647
Posted By GenoMax
It is an odd request but it should be possible....

It is an odd request but it should be possible. Someone one on experimental side will chip in to confirm.

On informatics side you will need make sure the SampleSheet is correctly set up. No...
Forum: General 09-17-2019, 04:03 PM
Replies: 14
Views: 1,660
Posted By GenoMax
Then we have been on wrong track all along. You...

Then we have been on wrong track all along. You should have said you need a consensus fasta file from the BAM alignment.

What you need is: https://www.biostars.org/p/367960/

I had posted this...
Forum: General 09-17-2019, 01:00 PM
Replies: 14
Views: 1,660
Posted By GenoMax
Output fasta reads were interleaved (put in one...

Output fasta reads were interleaved (put in one file) since you had paired-end reads to begin with. To separate them into two files you should use the command below.


for i in *.fa; do...
Forum: Bioinformatics 09-16-2019, 10:37 AM
Replies: 1
Views: 539
Posted By GenoMax
Cross-posted on biostars:...

Cross-posted on biostars: https://www.biostars.org/p/398986/
Forum: General 09-12-2019, 09:23 AM
Replies: 14
Views: 1,660
Posted By GenoMax
Good catch SNPsaurus. I have updated my original...

Good catch SNPsaurus. I have updated my original command. There was an additional ".bam" in there.

@Manuelly: Use for i in *.bam; do reformat.sh in=$i out=${i}.fa; done

If you are trying to...
Forum: General 09-10-2019, 09:57 AM
Replies: 2
Views: 1,291
Posted By GenoMax
You need to provide more information about what...

You need to provide more information about what software you are running, how you are running it. Is it custom code you wrote or a package that is available on web?
Forum: Bioinformatics 09-09-2019, 08:57 PM
Replies: 331
Views: 118,118
Posted By GenoMax
You can simply capture the STDERR output (where...

You can simply capture the STDERR output (where this is bring written) to a file (https://askubuntu.com/questions/625224/how-to-redirect-stderr-to-a-file).
Forum: Bioinformatics 08-30-2019, 12:05 AM
Replies: 2
Views: 618
Posted By GenoMax
Have you tried to see where (96-95-29.4) reads...

Have you tried to see where (96-95-29.4) reads are aligning (since they are not aligning to transcripts)? Does your data have rRNA present? Inspecting the resulting BAM using IGV would be a great...
Forum: General 08-28-2019, 09:30 AM
Replies: 14
Views: 1,660
Posted By GenoMax
Yes you can convert multiple files at once. If...

Yes you can convert multiple files at once. If your data came from paired-end reads then be aware that the "out=" files will contain data in interleaved format. You will need to separate R1/R2 reads....
Forum: General 08-27-2019, 04:52 PM
Replies: 14
Views: 1,660
Posted By GenoMax
Use reformat.sh from BBMap suite. Take a look at...

Use reformat.sh from BBMap suite. Take a look at BAM processing options in in-line help to decide if you want to keep primary reads etc.

for i in *.bam; do reformat.sh in=${i} out=${i}.fa...
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