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Search: Posts Made By: alexdobin
Forum: Bioinformatics 12-21-2016, 12:04 PM
Replies: 218
Views: 134,582
Posted By alexdobin
Hi Dietmar, the non-canonical junctions have...

Hi Dietmar,

the non-canonical junctions have non-canonical motifs, but they are still "linear" in the genome, i.e. acceptor site follows the donor site. The circular junctions are classified as...
Forum: Bioinformatics 12-12-2016, 10:06 AM
Replies: 20
Views: 13,212
Posted By alexdobin
Hi Nadia, if you your RNA-seq data is...

Hi Nadia,

if you your RNA-seq data is stranded, you need to run Cufflinks with --library-type option. If your RNA-seq data is unstranded, you have to run STAR with "--outSAMstrandField...
Forum: Bioinformatics 09-27-2016, 03:10 PM
Replies: 218
Views: 134,582
Posted By alexdobin
Hi, depending on the read length, the speed...

Hi,

depending on the read length, the speed should 20-50M reads per hour per core, so it should be doable. 32GB is just enough for human genome.

Cheers
Alex
Forum: Bioinformatics 07-08-2016, 12:32 PM
Replies: 2
Views: 1,582
Posted By alexdobin
Hi Matt, STAR will indeed re-start the...

Hi Matt,

STAR will indeed re-start the search for maximal mapped prefixes in the unmapped portion of the read. Moreover, the search is started not just at the beginning/end of the reads, but also...
Forum: Bioinformatics 05-04-2016, 08:31 AM
Replies: 218
Views: 134,582
Posted By alexdobin
Hi Sam, To avoid quantification bias it's...

Hi Sam,

To avoid quantification bias it's better to use the same splice junctions for the 2nd pass mapping. However, this affects only the novel (unannotated junctions), so if you are quantifying...
Forum: Bioinformatics 04-06-2016, 09:30 AM
Replies: 218
Views: 134,582
Posted By alexdobin
The new versions of STAR may not work with old...

The new versions of STAR may not work with old genome indexes in rare cases - hence my recommendation to re-generate with 2.5.1 that is very stable.
Forum: Bioinformatics 04-06-2016, 07:31 AM
Replies: 218
Views: 134,582
Posted By alexdobin
Hi Sam, this would be generally safe,...

Hi Sam,

this would be generally safe, however, when you publish your method, the reviewers and readers will have a bone to pick with you. :)
STAR does not really require installation, you can...
Forum: Bioinformatics 04-04-2016, 03:25 PM
Replies: 218
Views: 134,582
Posted By alexdobin
The file with parameters should have each...

The file with parameters should have each parameter on a separate line:
<parameterName> <parameterValue(s)>
parameterName should not contain --
For instance,
genomeChrBinNbits ...
Forum: Bioinformatics 02-29-2016, 09:17 AM
Replies: 2
Views: 1,144
Posted By alexdobin
Hi @Him26, please post or send me the...

Hi @Him26,

please post or send me the Log.out file, and also a few hundred lines. It's likely that the problem is with GTF file formatting.

Cheers
Alex
Forum: Bioinformatics 02-26-2016, 03:26 PM
Replies: 12
Views: 2,572
Posted By alexdobin
Hi @biokloot, the best way to suppress...

Hi @biokloot,

the best way to suppress detection of any new junctions in 2nd pass (i.e. junctions not detected in the 1st pass) is to use --alignSJoverhang 100000 (or any number > read length)....
Forum: Bioinformatics 02-24-2016, 01:12 PM
Replies: 1
Views: 1,461
Posted By alexdobin
Hi @Studentlost, I do not think you should...

Hi @Studentlost,

I do not think you should tweak mapping parameters for low complexity libraries. The presence of duplicates does not affect mapping since each read is mapped independently....
Forum: Bioinformatics 02-19-2016, 02:29 PM
Replies: 218
Views: 134,582
Posted By alexdobin
Hi Rui, here are a few suggestions in...

Hi Rui,

here are a few suggestions in addition to @GenoMax's suggestion.

1. You are using --alignEndsType EndToEnd, which requires end-to-end alignment for each read (no soft clipping). This...
Forum: Bioinformatics 02-11-2016, 08:57 AM
Replies: 12
Views: 2,572
Posted By alexdobin
Hi Rui, the --outSJfilterCountUniqueMin -1...

Hi Rui,

the --outSJfilterCountUniqueMin -1 -1 -1 -1 --outSJfilterCountTotalMin 10 10 10 10 filter will not apply to the "annotated" junctions, i.e. junctions that are introduced via...
Forum: Bioinformatics 02-10-2016, 08:02 AM
Replies: 12
Views: 2,572
Posted By alexdobin
Hi Rui, sorry, I forgot that...

Hi Rui,

sorry, I forgot that --outSJfilterCountUniqueMin and --outSJfilterCountTotalMin filters are used in the OR fashion, i.e. if one or the other is satisifed, the junction will be kept - so...
Forum: Bioinformatics 02-09-2016, 04:32 PM
Replies: 218
Views: 134,582
Posted By alexdobin
Hi @umn_bist STAR does not need or use the...

Hi @umn_bist

STAR does not need or use the "expected" insert length information for mapping - so yo do not have to worry about it. :)
For mapping of DNA-seq data we can decide whether an...
Forum: Bioinformatics 02-09-2016, 04:26 PM
Replies: 12
Views: 2,572
Posted By alexdobin
Hi @harrike, --outSJfilterCountUniqueMin 10...

Hi @harrike,

--outSJfilterCountUniqueMin 10 10 10 10 --outFilterType BySJout
will remove all junctions that are supported by <10 uniquely mapping reads. The 4 numbers are for different intron...
Forum: Bioinformatics 02-05-2016, 01:46 PM
Replies: 218
Views: 134,582
Posted By alexdobin
Hi @emixaM, with 24GB of RAM and human...

Hi @emixaM,

with 24GB of RAM and human genome you would need to use --genomeSAsparseD 2.
You do not need --genomeChrBinNbits 8 --limitIObufferSize 4000000000, and can increase ...
Forum: Bioinformatics 01-26-2016, 09:31 AM
Replies: 20
Views: 13,212
Posted By alexdobin
Hi LTR, the "--outSAMstrandField...

Hi LTR,

the "--outSAMstrandField intronMotif" option should produce XS flags for all spliced alignments. If you used this option and Cufflinks still complains about it, please send me the Log.out...
Forum: Bioinformatics 01-14-2016, 01:52 PM
Replies: 218
Views: 134,582
Posted By alexdobin
Hi @bastianwur, quoting from the manual: :) ...

Hi @bastianwur,

quoting from the manual: :)

"If you are using a genome with a large (>5,000) number of references (chrosomes/sca olds), you may need to reduce the --genomeChrBinNbits to reduce...
Forum: Bioinformatics 01-12-2016, 12:02 PM
Replies: 8
Views: 3,073
Posted By alexdobin
Hi @viktoriag, STAR GeneCount algorithm is...

Hi @viktoriag,

STAR GeneCount algorithm is very straightforward: all uniquely mapping reads that overlap exons of only one gene are counted. Multimapping reads are not counted, and reads...
Forum: Bioinformatics 12-30-2015, 01:24 PM
Replies: 8
Views: 3,073
Posted By alexdobin
Hi @analog900, I have mapped one of these...

Hi @analog900,

I have mapped one of these samples to m38 assembly with Gencode M8 annotations, and got 1.2M reads mapped uniquely, out of which 600k (50%) were "no feature", i.e. did not overlap...
Forum: Bioinformatics 12-23-2015, 04:05 PM
Replies: 8
Views: 3,073
Posted By alexdobin
Nothing suspicious in the summary statistics... ...

Nothing suspicious in the summary statistics...
It might be a problem with annotations - could you point me to the genome/annotations you were using? And also the public .fastq files you mentioned.
Forum: Bioinformatics 12-23-2015, 11:27 AM
Replies: 8
Views: 3,073
Posted By alexdobin
Hi @analog900 could you please post...

Hi @analog900

could you please post Log.final.out file and the first 4 lines of the ReadsPerGene.out.tab file?

Cheers
Alex
Forum: RNA Sequencing 12-16-2015, 01:31 PM
Replies: 1
Views: 1,615
Posted By alexdobin
Hi @lre1234 you can feed a properly...

Hi @lre1234

you can feed a properly formatted GFF3 file directly to STAR with --sjdbGTFfile /path/to/annot.gff3 --sjdbGTFtagExonParentTranscript Parent , and STAR will extract the junctions from...
Forum: Bioinformatics 12-07-2015, 03:20 PM
Replies: 218
Views: 134,582
Posted By alexdobin
Hi Yasser, at the moment the best option is...

Hi Yasser,

at the moment the best option is to convert GFF3 file into GTF file.
For instance, you can use gffread tool from Cufflinks package:
$ gffread -T annot.gff3 -o annot.gtf
It creates...
Showing results 1 to 25 of 161

 


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