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Search: Posts Made By: splaisan
Forum: Bioinformatics 08-13-2018, 01:25 AM
Replies: 4
Views: 7,386
Posted By splaisan
legacy Blast has a new home, close to the old one

the link is slightly different after deprecation of legacy Blast
look into:

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/
Forum: Bioinformatics 07-18-2018, 04:43 AM
Replies: 12
Views: 4,191
Posted By splaisan
one way to get it

see https://www.biostars.org/p/17575/#327644
Forum: Bioinformatics 09-05-2017, 01:45 AM
Replies: 0
Views: 1,765
Posted By splaisan
Method for comparing denovo to reference assembly

I obtained a non-sorted assembly (contigs) which I would like to:
* compare to the expected reference genome (available as fasta, gff, gbk)
* sort and re-orientate the contigs to best match the...
Forum: Bioinformatics 03-25-2017, 06:20 AM
Replies: 0
Views: 2,704
Posted By splaisan
variant calling from pacBio Sequel data

I am struggling with variant calling in 'Re-sequencing' mode using SMRT v4 and so far found that the VCF format generate by SMRTv4 is not valid.
Their VCF v3.3 is a non-documented weird version...
Forum: Bioinformatics 03-22-2017, 01:41 AM
Replies: 4
Views: 9,096
Posted By splaisan
In my hands, the VCF v3.3 (exotic version if one...

In my hands, the VCF v3.3 (exotic version if one with weird call syntax for the ALT field) format produced by SMRTv4 accompanying gffToVcf (v3.0 - pbgenomicconsensus) is not conform to the VCF4 specs...
Forum: Bioinformatics 10-06-2016, 05:20 AM
Replies: 3
Views: 1,348
Posted By splaisan
Thanks @kmcarr, this looks indeed nice too but...

Thanks @kmcarr, this looks indeed nice too but will require some setup to bring the two entities to life. I should look at this once but my small needs are satisfied with the simplistic multifasta...
Forum: Bioinformatics 10-06-2016, 01:37 AM
Replies: 3
Views: 1,348
Posted By splaisan
And the winner is .... put all queries in a...

And the winner is ....
put all queries in a single multifasta.
so simple I did not think about it.

shame on me :-(
Forum: Bioinformatics 10-06-2016, 01:24 AM
Replies: 3
Views: 1,348
Posted By splaisan
keep .2bit reference in memory during batch blat jobs

I succeeded to run a single blat search with standalone blat installed but would like to reduce the time of loading the reference each time when doing consecutive searches from a list of queries.
...
Forum: Bioinformatics 05-05-2015, 02:37 AM
Replies: 3
Views: 1,562
Posted By splaisan
Thanks Ryan but I did not ask if duplicates...

Thanks Ryan but I did not ask if duplicates should be removed which I know they should not be.
Forum: Bioinformatics 05-05-2015, 12:07 AM
Replies: 3
Views: 1,562
Posted By splaisan
what happens with read duplicates?

I routinely mark (I do not delete) my duplicate reads using Picard MarkDuplicate wether I do gDNA seq or RNA Seq but I still ignore (besides for GATK) which downstream software do take the marking...
Forum: Bioinformatics 05-22-2014, 02:40 AM
Replies: 0
Views: 843
Posted By splaisan
Cool looking for illumina fastq RNASeq data with errors

:confused:Hi,

In order to demonstrate the need for pre-procesing of illumina RNASeq reads to a biologist class, I would like to identify a good example of dirty data ;-) to which I could apply...
Forum: RNA Sequencing 02-15-2014, 05:15 AM
Replies: 5
Views: 1,522
Posted By splaisan
shame on me! corrected now (thanks)

shame on me! corrected now (thanks)
Forum: RNA Sequencing 02-15-2014, 12:59 AM
Replies: 5
Views: 1,522
Posted By splaisan
picard markDuplicate compatible reads from SRA data

few days later, the issue is fixed by:


NOT downloading the fastq files from SRA but instead the .sra formatted data using Aspera (I used the browser link)
Use the sratoolkit command...
Forum: RNA Sequencing 02-13-2014, 05:58 AM
Replies: 5
Views: 1,522
Posted By splaisan
Problem is I downloaded the fastq pre-made from...

Problem is I downloaded the fastq pre-made from the EBI repo and mapped them all :-( without figuring this out. I can fix this by patching the fatsQ but will still need to remap the whole shebang......
Forum: RNA Sequencing 02-13-2014, 05:30 AM
Replies: 5
Views: 1,522
Posted By splaisan
keep read address using tophat

Maybe overlooking something but ...
when I use tophat with paired reads having a name as

I end up with the second part clipped and a arbitrary read number put instead in the resulting bam as...
Forum: General 12-19-2013, 12:34 AM
Replies: 4
Views: 2,956
Posted By splaisan
how much of the MHC is represented in the reference genome?

I remember that former versions of the reference genome (at least hg18) used to lack some genes due to compression of the sequences to one prototype in the case of closely located repeated 'genes'. ...
Forum: General 12-06-2013, 02:29 AM
Replies: 3
Views: 3,083
Posted By splaisan
Thanks for this answer, it already sheds some...

Thanks for this answer, it already sheds some light.

No part is unsatisfactory but the process leading to a wrong estimate is not really explained (or I did not understand it correctly). Is it...
Forum: General 12-06-2013, 01:54 AM
Replies: 3
Views: 3,083
Posted By splaisan
why should BAM be shuffled before extracting to FASTQ?

I came across this apparent bias when recovering FASTQ paired read data from BAM for re-mapping purpose (public data obtained from SRA or new reference genome available).

It seems that if I...
Forum: Bioinformatics 10-31-2013, 04:11 AM
Replies: 3
Views: 4,761
Posted By splaisan
Smile adding @PG @RG and more with BamUtil polishBam

I disc-overed this great 'Umich' tooolbox after searching for quite some time (http://genome.sph.umich.edu/wiki/BamUtil:_polishBam)

I first stored my full bwa command in a variable 'cmd' then...
Forum: Bioinformatics 10-16-2013, 05:18 AM
Replies: 5
Views: 3,026
Posted By splaisan
Thanks a LOT Devon, I added -h to the...

Thanks a LOT Devon,

I added -h to the upstream samtools view cmd to forward the sam header and 'continue' to the code to process header lines and directly go to the next loop

for read in f :
...
Forum: Bioinformatics 10-16-2013, 01:45 AM
Replies: 5
Views: 3,026
Posted By splaisan
I would like to learn how to clean that file in...

I would like to learn how to clean that file in order to be able to redo such operation with future data having similar issues.

Thanks for the links anyway.:)
Forum: Bioinformatics 10-16-2013, 01:21 AM
Replies: 5
Views: 3,026
Posted By splaisan
cleaning partial PE sam data

Hello there,
I obtained PE data from Illumina (chr21 subset of NA18507 - ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/NA18507_GAIIx_100_chr21.bam).

After a lot of misery and...
Forum: Bioinformatics 10-29-2012, 04:33 AM
Replies: 0
Views: 1,083
Posted By splaisan
what does tophat '--coverage-search'

I tried to figure out what the consequences are in using --coverage-search vs --no-coverage-search.
Tophat warns me each run that with --no-coverage-search it will go faster but nowhere did I find...
Forum: RNA Sequencing 10-23-2012, 06:03 AM
Replies: 0
Views: 1,017
Posted By splaisan
importance of balancing read counts?

Hi,

I wonder what the effect is of running a tophat..cuffdiff analysis with single-end read groups of quite different size.

One of our library/sample is 3x larger in read count than the others....
Forum: Bioinformatics 01-31-2012, 12:10 AM
Replies: 4
Views: 2,222
Posted By splaisan
Smile thanks Heng

This helps a lot and I will alias it for regular use!
You just saved me several gigabites of disk space.
Cool
Stephane
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