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Search took 0.06 seconds. Search: Posts Made By: GenoMax
Forum: Bioinformatics Today, 01:13 PM
Replies: 1
Views: 33
Posted By GenoMax
Why not ask them to export the normalized values...

Why not ask them to export the normalized values from CLC (or better still the raw counts). You can do your own analysis (sounds like you are comfortable with R) with that data (e.g. DESeq2).
Forum: Bioinformatics 07-07-2017, 06:47 PM
Replies: 1
Views: 278
Posted By GenoMax
For reference cross-posted on Biostars:...

For reference cross-posted on Biostars: https://www.biostars.org/p/261406/
Forum: RNA Sequencing 07-06-2017, 06:30 PM
Replies: 5
Views: 366
Posted By GenoMax
See this article for some pointers...

See this article for some pointers (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728800/).

You could be strict and drop them altogether, allow the aligner to randomly pick one spot (out of many...
Forum: Illumina/Solexa 07-05-2017, 07:25 PM
Replies: 6
Views: 333
Posted By GenoMax
It is true that shorter inserts tend to cluster...

It is true that shorter inserts tend to cluster more efficiently on the flowcell than longer ones. You could use less amounts of shorter ones and try to bias a uniform representation.

Someone...
Forum: RNA Sequencing 07-05-2017, 07:00 PM
Replies: 5
Views: 366
Posted By GenoMax
One would think so but that may always not be the...

One would think so but that may always not be the case. You should check what the multi-mapping reads are? Ideally aligning against rDNA repeat (from your species) would give you an exact idea of how...
Forum: Illumina/Solexa 07-05-2017, 06:58 PM
Replies: 9
Views: 503
Posted By GenoMax
I concur with @Brian. You should analyze the data...

I concur with @Brian. You should analyze the data and then see if there are any particular issues noted with the results.
Forum: Illumina/Solexa 07-05-2017, 06:56 PM
Replies: 6
Views: 333
Posted By GenoMax
What kind of sequencing bias are you referring...

What kind of sequencing bias are you referring to? If you are going to be mixing products of different length then even the low nucleotide diversity (which may be an issue with amplicon sequencing)...
Forum: RNA Sequencing 07-05-2017, 07:37 AM
Replies: 5
Views: 366
Posted By GenoMax
Were these libraries ribo-depleted? If not the...

Were these libraries ribo-depleted? If not the multi-mapping reads could be from rRNA.
Forum: Bioinformatics 07-05-2017, 07:35 AM
Replies: 8
Views: 495
Posted By GenoMax
The command I had posted is for using in a shell....

The command I had posted is for using in a shell. You should be able to figure out the R equivalent from subread vignette.

You would need to find a GTF for the genome build that was used to...
Forum: Bioinformatics 07-04-2017, 04:22 PM
Replies: 8
Views: 495
Posted By GenoMax
It is not that difficult if you have some command...

It is not that difficult if you have some command like skills. If not, can you do R? There is an R package for subread/featurecounts that could be used instead.

All you basically need to do is...
Forum: Bioinformatics 07-03-2017, 07:15 PM
Replies: 8
Views: 495
Posted By GenoMax
featureCounts...

featureCounts (http://bioinf.wehi.edu.au/featureCounts/) manual.
Forum: Bioinformatics 06-30-2017, 07:57 AM
Replies: 245
Views: 51,017
Posted By GenoMax
You can use a standard unix loop to iterate over...

You can use a standard unix loop to iterate over all files, grab the file basenames and use them in individual bbmap tools.
Forum: Bioinformatics 06-29-2017, 07:29 PM
Replies: 245
Views: 51,017
Posted By GenoMax
Can you dump these reads with "-F" option for...

Can you dump these reads with "-F" option for fastq-dump to see if you are able to restore the original Illumina fastq headers. repair.sh should (if needed) work after that.
Forum: Bioinformatics 06-29-2017, 07:27 PM
Replies: 2
Views: 290
Posted By GenoMax
While algorithms can get you to/near a reasonable...

While algorithms can get you to/near a reasonable solution, it may not always be the best/correct. Manual inspection/editing of the alignments (since you can consider biological context e.g. presence...
Forum: Bioinformatics 06-25-2017, 03:07 PM
Replies: 2
Views: 285
Posted By GenoMax
Looks like the output is specified as (/dev/null...

Looks like the output is specified as (/dev/null = nothing). Change that to a real path/file name e.g. /home/ubuntu/GSoC-Strain_Diffrential/test_modified.vcf.gz
Forum: Introductions 06-25-2017, 10:13 AM
Replies: 2
Views: 263
Posted By GenoMax
You appear to have one read (at least) where the...

You appear to have one read (at least) where the sequence length does not match the quality score line length (corrupt fastg record). You can do something like $ grep -A 3...
Forum: Metagenomics 06-23-2017, 03:28 AM
Replies: 2
Views: 311
Posted By GenoMax
Someone else will comment on experimental tricks...

Someone else will comment on experimental tricks to mitigate this issue but I wanted to mention BBSplit from BBMap suite which is designed for exactly this bioinformatics task. You can find the...
Forum: Pacific Biosciences 06-22-2017, 04:05 AM
Replies: 7
Views: 408
Posted By GenoMax
Have you contacted PacBio tech support directly...

Have you contacted PacBio tech support directly about this?

While it is common to see some sequences getting assigned to indexes you did not use, you should obviously get the correct results, if...
Forum: Pacific Biosciences 06-22-2017, 03:57 AM
Replies: 9
Views: 360
Posted By GenoMax
@gringer: In addition to the pure cost/yield for...

@gringer: In addition to the pure cost/yield for MinION can you comment on (if you have experience) chances of MinION data successfully able to "close" the microbial genomes? That appears to be a...
Forum: RNA Sequencing 06-21-2017, 10:47 AM
Replies: 2
Views: 216
Posted By GenoMax
You should try a non-gapped aligner like bowtie...

You should try a non-gapped aligner like bowtie v.1 for this. Be sure to remove/trim any kit specific adapters/illumina adapters before alignment.
Forum: Bioinformatics 06-21-2017, 08:40 AM
Replies: 5
Views: 207
Posted By GenoMax
Examine your ID file (something like cat -vet...

Examine your ID file (something like cat -vet yourFile) to see if there are any non-printable characters that could be causing potential issues.
Forum: Bioinformatics 06-21-2017, 08:22 AM
Replies: 1
Views: 184
Posted By GenoMax
I answered your identical question on Biostars:...

I answered your identical question on Biostars: https://www.biostars.org/p/258576/ already.
Forum: Bioinformatics 06-21-2017, 06:17 AM
Replies: 5
Views: 207
Posted By GenoMax
Tested and appears to work fine. Fasta ID's need...

Tested and appears to work fine. Fasta ID's need to match exactly (unless you want to try reg exp/wild cards).

$ more list.fa
>JFCCLHHB_00692
AGCTCGAT
>CKEMPBAI_00693
ACGCTG
>FBNBCCDE_01742...
Forum: Bioinformatics 06-21-2017, 05:50 AM
Replies: 5
Views: 207
Posted By GenoMax
Are you referring to samtools faidx or something...

Are you referring to samtools faidx or something else?
Forum: Bioinformatics 06-20-2017, 10:32 AM
Replies: 1
Views: 125
Posted By GenoMax
A vcf file should be plain text (unless...

A vcf file should be plain text (unless compressed) so there is something wrong. What version of samtools/bcftools are you using? If not the latest I would suggest you try upgrading first.
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