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Search: Posts Made By: GenoMax
Forum: Bioinformatics Yesterday, 03:50 AM
Replies: 665
Views: 150,441
Posted By GenoMax
If your OS does not support shellscripts, replace...

If your OS does not support shellscripts, replace 'bbmap.sh' like this:
java -XmxNNg -cp /path/to/current align2.BBMap in=reads.fq out=mapped.sam

(NN will be a real number on your system).
Forum: Illumina/Solexa 03-13-2019, 06:49 AM
Replies: 2
Views: 169
Posted By GenoMax
It should basically be very similar to other...

It should basically be very similar to other Illumina sequencers. Quality scores on NovaSeq are binned by default so they would not be directly comparable. BBMap may be able to recalibrate the scores...
Forum: Bioinformatics 03-12-2019, 07:08 AM
Replies: 1
Views: 128
Posted By GenoMax
Cross-posted on Biostars, see my answer there:...

Cross-posted on Biostars, see my answer there: https://www.biostars.org/p/369000/#369008
Forum: General 03-11-2019, 06:37 AM
Replies: 5
Views: 173
Posted By GenoMax
If this is an assignment then use what you have...

If this is an assignment then use what you have to but comm should work (as long as you have enough RAM available). Since you are working with only read names (if you are not then you should).
Forum: General 03-11-2019, 06:06 AM
Replies: 5
Views: 173
Posted By GenoMax
You could simply get the names (field 1 as you...

You could simply get the names (field 1 as you already note, sort | uniq them in bash) and do a "comm" comparison of the three results. If your aim is just to find which reads are present in all...
Forum: Illumina/Solexa 03-07-2019, 03:59 AM
Replies: 4
Views: 436
Posted By GenoMax
If you use your MiSeq consistently (at least once...

If you use your MiSeq consistently (at least once a week) investing in the higher level contract with PM may be useful. Consider it cost of doing business and roll that into your operating costs.
Forum: RNA Sequencing 03-05-2019, 08:54 AM
Replies: 5
Views: 219
Posted By GenoMax
You can use DESeq2 without replicates...

You can use DESeq2 without replicates (https://support.bioconductor.org/p/101210/). It is not recommended. Your analysis would not have any statistical significance.

Hopefully you have some other...
Forum: RNA Sequencing 03-05-2019, 07:49 AM
Replies: 5
Views: 219
Posted By GenoMax
You will get raw counts from featureCounts. You...

You will get raw counts from featureCounts. You will need to use DESeq2/edgeR etc to actually do normalization and analysis.
Forum: RNA Sequencing 03-05-2019, 07:37 AM
Replies: 5
Views: 219
Posted By GenoMax
featureCounts part of Subread package...

featureCounts part of Subread package (http://subread.sourceforge.net/). You can feed all your BAM files at the same time to get a matrix of counts (rows as genes and columns as your samples).
Forum: RNA Sequencing 03-05-2019, 03:59 AM
Replies: 1
Views: 245
Posted By GenoMax
You can use Integrated Genome Viewer (Broad...

You can use Integrated Genome Viewer (Broad Institute) to do batch analyses/exports of images. Details are included here (https://software.broadinstitute.org/software/igv/batch).
...
Forum: Bioinformatics 03-04-2019, 05:53 AM
Replies: 9
Views: 398
Posted By GenoMax
Are you running this on a cluster/remote server?...

Are you running this on a cluster/remote server? Perhaps your process is encountering disk quota limit?
Forum: Bioinformatics 03-04-2019, 04:18 AM
Replies: 9
Views: 398
Posted By GenoMax
Are your data files very large? If the SAM file...

Are your data files very large? If the SAM file being made gets very large then you could possibly run into a space issue.
Forum: Bioinformatics 03-03-2019, 04:22 PM
Replies: 9
Views: 398
Posted By GenoMax
That is odd because the error says that hisat is...

That is odd because the error says that hisat is unable to read this file.


Warning: Could not open read file "/home/RNA-seq/Human/eynden/clb-bar-ctrl.fastq" for reading; skipping...
Error: No...
Forum: Bioinformatics 03-03-2019, 12:35 PM
Replies: 9
Views: 398
Posted By GenoMax
Are you trying to pass more than one set of files...

Are you trying to pass more than one set of files in your command line? Can you post your command line?
Forum: Illumina/Solexa 03-03-2019, 04:54 AM
Replies: 2
Views: 391
Posted By GenoMax
Have you consulted Illumina tech support? You are...

Have you consulted Illumina tech support? You are not doing something totally custom that is unsupported by Illumina?
Forum: Illumina/Solexa 02-28-2019, 02:25 PM
Replies: 3
Views: 451
Posted By GenoMax
Interesting. Let us know what happens.

Interesting. Let us know what happens.
Forum: General 02-28-2019, 02:25 PM
Replies: 2
Views: 319
Posted By GenoMax
If you know the barcode sequences you may be able...

If you know the barcode sequences you may be able to use bbduk.sh from BBMap suite to bin the reads you are interested in.
Forum: Illumina/Solexa 02-28-2019, 07:27 AM
Replies: 3
Views: 451
Posted By GenoMax
Sounds like bcl2fastq experienced a software...

Sounds like bcl2fastq experienced a software issue. I suggest that you re-run the demultiplexing. I have seen this posted rarely and if I recall had experienced it one time. bcl2fastq re-run fixed...
Forum: General 02-28-2019, 05:20 AM
Replies: 4
Views: 857
Posted By GenoMax
It depends. If you want a quick scan you could...

It depends. If you want a quick scan you could use something like fastq screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/). You will need to select the database carefully.
...
Forum: Bioinformatics 02-26-2019, 04:42 AM
Replies: 327
Views: 98,482
Posted By GenoMax
@aushev: Unfortunately Brian no longer has time...

@aushev: Unfortunately Brian no longer has time to participate on this forum. He would really be the only person who can authoritatively answer your questions. You could try to create a ticket on SF...
Forum: Bioinformatics 02-25-2019, 04:11 PM
Replies: 327
Views: 98,482
Posted By GenoMax
Any reads that align to the ribosomal repeat will...

Any reads that align to the ribosomal repeat will be identified and separated in a file. Isn't that what you are looking to do?
Forum: Bioinformatics 02-25-2019, 11:12 AM
Replies: 327
Views: 98,482
Posted By GenoMax
@aushev: That k-mers file is likely for non-human...

@aushev: That k-mers file is likely for non-human genomes since it was made from SILVA database.

You could use U13369 fasta sequence and then bin the reads that map to it using bbsplit.sh.
Forum: Bioinformatics 02-25-2019, 03:24 AM
Replies: 96
Views: 19,469
Posted By GenoMax
@Dario1984: Have you run clumpify on your data?...

@Dario1984: Have you run clumpify on your data? If you have excellent libraries with tightly controlled insert sizes you will find the duplicate rate to be well controlled. Brian has some explicit...
Forum: RNA Sequencing 02-24-2019, 03:43 PM
Replies: 2
Views: 342
Posted By GenoMax
You are confusing technical replicates with...

You are confusing technical replicates with biological ones. What you want is biological replicates (which some GEO data may have). People rarely do technical replicates now a days.
Forum: Bioinformatics 02-24-2019, 06:49 AM
Replies: 128
Views: 52,739
Posted By GenoMax
@Shriram369: As long as your reads are in proper...

@Shriram369: As long as your reads are in proper order in the files it would be fine to sub-set the data into manageable chunks and then do the merging.
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