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Forum: Illumina/Solexa Today, 06:00 AM
Replies: 5
Views: 93
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 Today, 05:11 AM
Replies: 5
Views: 93
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 Today, 03:20 AM
Replies: 5
Views: 93
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: 145
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: 245
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: 1
Views: 240
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: 586
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: 637
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: 637
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: 1,281
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: 7,478
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: 7,478
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: 1,407
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: 4
Views: 595
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: 1,116
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: 736
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: 1,116
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: 1,116
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...
Forum: Bioinformatics 08-02-2018, 05:08 AM
Replies: 25
Views: 15,549
Posted By GenoMax
You can use reformat.sh in=your_file.fastq...

You can use reformat.sh in=your_file.fastq out=newfile.fa to convert the reads to fasta format.

That said I think mapPacBio.sh should automatically split reads longer than 6k when it does...
Forum: Bioinformatics 07-31-2018, 03:29 AM
Replies: 5
Views: 736
Posted By GenoMax
Before we get into specifics can you ask your...

Before we get into specifics can you ask your sequence provider to do this demultiplexing with Illumina's program called bcl2fastq (you can't do this since it requires access to the full data folder...
Forum: Bioinformatics 07-23-2018, 10:15 AM
Replies: 90
Views: 15,115
Posted By GenoMax
I am able to do something like for i in `ls...

I am able to do something like

for i in `ls -1 *_1*.fastq | sed 's/_1.fastq//'`; do clumpify.sh -Xmx10g in1=$i\_1.fastq in2=$i\_2.fastq out1=$i\_clu_1.fastq out2=$i\_clu_2.fastq; done and have...
Forum: Bioinformatics 07-21-2018, 05:31 AM
Replies: 90
Views: 15,115
Posted By GenoMax
Are you using the latest version of BBMap? Have...

Are you using the latest version of BBMap? Have you tried to run a test with actual file names instead of shell variables?
Forum: Bioinformatics 07-21-2018, 04:16 AM
Replies: 90
Views: 15,115
Posted By GenoMax
It looks like out1= and out2= variables are not...

It looks like out1= and out2= variables are not being correctly expanded. BBMap seems to think that your outputs are inputs (in1=./Preproccesing/ERR522065/ERR522065_1_optical.fastq.gz,...
Forum: Bioinformatics 07-19-2018, 11:02 AM
Replies: 2
Views: 334
Posted By GenoMax
Help page ...

Help page (https://software.broadinstitute.org/software/igv/interpreting_insert_size)that describes the meaning of those colors.
Forum: Bioinformatics 07-19-2018, 03:59 AM
Replies: 1
Views: 351
Posted By GenoMax
I am not seeing anything that is an obvious red...

I am not seeing anything that is an obvious red flag. Getting warning in FastQC analysis is common and those need to be taken into consideration using the context of your experiment.

You will...
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