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Forum: Illumina/Solexa 10-12-2018, 06:24 AM
Replies: 2
Views: 236
Posted By GenoMax
This data must have been sequenced on NextSeq (or...

This data must have been sequenced on NextSeq (or NovaSeq). That string of "G" is probably no-signal which is interpreted as G base.

The bias at the beginning of the reads is likely due to the...
Forum: Illumina/Solexa 10-09-2018, 08:29 AM
Replies: 2
Views: 151
Posted By GenoMax
1. Yes (AFAIK). 2. Quality will be lower for...

1. Yes (AFAIK).
2. Quality will be lower for the last set of cycles. Depending on your library quality (and nucloetide diversity) that effect may be more or less pronounced.
3. Index reads are...
Forum: Bioinformatics 10-04-2018, 04:41 AM
Replies: 307
Views: 83,397
Posted By GenoMax
@FlySquirrelFly: It has become difficult to get a...

@FlySquirrelFly: It has become difficult to get a hold of Brian (due to his day job responsibilities) but I will flag your post for him to see if he can respond.

I recall from some past discussion...
Forum: Bioinformatics 09-27-2018, 05:31 PM
Replies: 2
Views: 258
Posted By GenoMax
Search EBI-ENA for minION. Here is a...

Search EBI-ENA for minION. Here is a representative search (https://www.ebi.ac.uk/ena/data/search?query=minion%2C+bacteria). Click on categories on the left (experiment is a good one).
Forum: Bioinformatics 09-27-2018, 04:23 AM
Replies: 4
Views: 258
Posted By GenoMax
This may be easier to do by obtaining the index...

This may be easier to do by obtaining the index read as a separate fastq file. You will also get real Q-scores for bases in index read when you do that. Stand-alone bcl2fastq allows one to get data...
Forum: Bioinformatics 09-26-2018, 11:01 AM
Replies: 4
Views: 258
Posted By GenoMax
Are you sure about that? Generally in case of...

Are you sure about that? Generally in case of Illumina sequencing index sequences (which are not part of actual reads) are transferred to the fastq header as a part of demultiplexing process. That is...
Forum: Bioinformatics 09-26-2018, 03:07 AM
Replies: 1
Views: 128
Posted By GenoMax
I am not sure what the size of BAM file you are...

I am not sure what the size of BAM file you are trying to use is but you could try adding the option "--java-mem-size=16G" to your qualimap command (Adjust RAM amount as needed). and see if that...
Forum: Illumina/Solexa 09-24-2018, 06:00 AM
Replies: 7
Views: 361
Posted By GenoMax
While likely let us hope that is not the case...

While likely let us hope that is not the case because otherwise you would be losing a lot of data to adapters and would have short reads.

When you have had a chance to investigate let us know...
Forum: Illumina/Solexa 09-24-2018, 05:11 AM
Replies: 7
Views: 361
Posted By GenoMax
Low nucleotide diversity in this case means...

Low nucleotide diversity in this case means majority of clusters will have e.g. an "A". When that happens the ability of the image analysis software to distinguish among clusters is hampered which...
Forum: Illumina/Solexa 09-24-2018, 03:20 AM
Replies: 7
Views: 361
Posted By GenoMax
1. Are these amplicons or sequences where there...

1. Are these amplicons or sequences where there is low nucleotide diversity expected?
2. You possibly have short inserts. Once you go through your inserts you are then sequencing into the adapter on...
Forum: RNA Sequencing 09-20-2018, 04:22 AM
Replies: 1
Views: 263
Posted By GenoMax
featureCounts is going to count reads per feature...

featureCounts is going to count reads per feature ("-t exon") that you specify and then will summarize the counts per gene ("-g gene_id"). It is going to report raw read counts and does not normalize...
Forum: Bioinformatics 09-09-2018, 07:30 AM
Replies: 1
Views: 334
Posted By GenoMax
I would suggest that you use the Illumina...

I would suggest that you use the Illumina provided adapter sequence. BBMerge detection feature is good when you don't have that information a priori. There may be some sequencing errors in your reads...
Forum: Illumina/Solexa 09-02-2018, 04:53 AM
Replies: 2
Views: 427
Posted By GenoMax
You just have to live with the quality of the...

You just have to live with the quality of the reads you get. Illumina requires 25 cycles in first read to accurately calibrate Q scores. Your type of sequencing is common with "Drop-seq" like methods...
Forum: Illumina/Solexa 08-21-2018, 11:24 AM
Replies: 5
Views: 671
Posted By GenoMax
If you are referring to sequences in...

If you are referring to sequences in "undetermined" files then these reads contain indexes that don't fit expected results (based on the samplesheet that you provide that has SampleID_Index mapping)....
Forum: Bioinformatics 08-14-2018, 03:21 AM
Replies: 3
Views: 661
Posted By GenoMax
You can try running the job again while nothing...

You can try running the job again while nothing else is running on the machine. You may be able to just get away with it.
Forum: Bioinformatics 08-13-2018, 11:02 AM
Replies: 3
Views: 661
Posted By GenoMax
Does 4TB refer to disk space? bwa is looking for...

Does 4TB refer to disk space? bwa is looking for more RAM so my guess is you don't have 53G of free RAM available or you are not the only user on this server.
Forum: Pacific Biosciences 08-12-2018, 03:29 PM
Replies: 4
Views: 1,353
Posted By GenoMax
Appears to some kind of file permission issue....

Appears to some kind of file permission issue. You should report this to PacBio tech support directly.
Forum: Bioinformatics 08-12-2018, 03:27 PM
Replies: 26
Views: 7,595
Posted By GenoMax
"bbsplit.sh" is a general purpose tool that will...

"bbsplit.sh" is a general purpose tool that will bin reads into any number of bins (depending on the reference sequences provided, you can provide as many as you want). In this case you would provide...
Forum: Bioinformatics 08-12-2018, 05:01 AM
Replies: 26
Views: 7,595
Posted By GenoMax
Have you tried using "bbsplit.sh" with human...

Have you tried using "bbsplit.sh" with human genome to see if that works better. If you are interested in non-human data then I would use the non-masked genome and risk losing a few additional reads.
Forum: Introductions 08-10-2018, 09:39 AM
Replies: 3
Views: 1,478
Posted By GenoMax
@Gabriela: Take a look at http://allseq.com/ and...

@Gabriela: Take a look at http://allseq.com/ and https://genohub.com/ to do comparison shopping for sequencing prices.

You should always have at least 3 (or more if possible) biological replicates...
Forum: Bioinformatics 08-10-2018, 04:00 AM
Replies: 5
Views: 725
Posted By GenoMax
@landrjos: What you are describing is called an...

@landrjos: What you are describing is called an interleaved fastq file where R1 and R2 reads are present in a single file.

You can use reformat.sh from BBMap suite...
Forum: Illumina/Solexa 08-07-2018, 06:19 AM
Replies: 11
Views: 1,195
Posted By GenoMax
Glad to hear they are doing the right thing and...

Glad to hear they are doing the right thing and will re-sequence. Only thing you are out of is time.
Forum: Bioinformatics 08-03-2018, 05:16 AM
Replies: 5
Views: 765
Posted By GenoMax
Your indexes most likely look like Index1+Index2...

Your indexes most likely look like Index1+Index2 (e.g. GGACTCCT+GCGATCTA) then that is how you need to include them in the file one per line. Is that how you are doing this?
Forum: Illumina/Solexa 08-02-2018, 07:14 AM
Replies: 11
Views: 1,195
Posted By GenoMax
As you appropriately said above: That...

As you appropriately said above:



That needs to take priority.
Forum: Illumina/Solexa 08-02-2018, 07:01 AM
Replies: 11
Views: 1,195
Posted By GenoMax
You can use "filterbytile.sh" from BBMap suite...

You can use "filterbytile.sh" from BBMap suite (https://sourceforge.net/projects/bbmap/).

Has the sequence provider said anything about the possibility that there was a hardware/software problem...
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