User: blaise.li__biostars

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France
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1 year, 4 months ago
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3 years, 10 months ago
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Posts by blaise.li__biostars

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Will Python Take The Place Of R?
... If I may add my testimony from 3 years later: In the last 3 years, I completely switched from python 2 to python 3, I learned a bit of R, used it for a few months, and, given the pain it was to do some programming with it, I finally decided to learn pandas and rpy2 to avoid having to deal with R as ...
written 16 months ago by blaise.li__biostars50
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Comment: C: How do I generate all possible Newick Tree permutations for a set of species giv
... Note that, for some reason, this solution does not seem to generate all possible results when polytomies are allowed. I found more topologies with this approach: https://stackoverflow.com/a/46707857/1878788] ...
written 17 months ago by blaise.li__biostars50
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Answer: A: Efficiently Iterating Over Fastq Records From Python
... In this [recent bioinformatics SE answer](https://bioinformatics.stackexchange.com/a/380/292), I tried the new (as of June 2017) python API for [GATB](http://gatb.inria.fr/). It contains a fasta/fastq parser module called "Bank" that seems quite fast. For instance, to only print reads longer than 6 ...
written 21 months ago by blaise.li__biostars50
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Comment: C: Preparation for Bioinformatics.SE closing
... Depends what SE site. StackOverflow has this tendency, but I find that this is not the case in biology SE, where users usually comment on how to improve a question rather than downvote. ...
written 21 months ago by blaise.li__biostars50
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Comment: C: How are tss_id gtf attributes determined? How do they relate to TSS annotations?
... Thanks for clarifying what tss_id and p_id correspond to and for the potentially useful script. You say that a given tss_id refers to a same start position of the first exon. In the particular case of C. elegans, many genes are subject to trans-splicing: the 5' end of the transcript is replaced by ...
written 2.3 years ago by blaise.li__biostars50
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How are tss_id gtf attributes determined? How do they relate to TSS annotations?
... A GTF file I have downloaded from iGenome contains a "tss_id" attribute. I suspect this is to match different annotated feature based on the fact that they are relative to a same transcript, i.e. the transcript they relate to come from a same transcription start site (TSS). Am I correct? How is th ...
rna-seq written 2.3 years ago by blaise.li__biostars50 • updated 2.3 years ago by Malcolm.Cook1.0k
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Answer: A: Small rna seq- counting multimapped tRNA fragments
... I made a pipeline adapted to small RNA-seq with multimapped reads. It is based on bowtie2, allowing reads to map at up to 10 locations (option -k 10), but keeping only best-scoring ex-aequo. If I remember well, I divided the contribution of a given read to the total counts by the number of such ex-a ...
written 2.4 years ago by blaise.li__biostars50
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Answer: A: Tophat on Debian Jessie installlation problem
... Solution found here: https://github.com/infphilo/tophat/pull/13   I managed compiling a fork that uses a newer SeqAn version: git clone https://github.com/wookietreiber/tophat.git cd tophat git checkout update-seqan ./bootstrap ./configure <insert your options here> make make install   ...
written 3.1 years ago by blaise.li__biostars50
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Answer: A: Tophat on Debian Jessie installlation problem
... For the record, I confirm the error for me on Debian:   ^ In file included from ./SeqAn-1.3/seqan/file.h:56:0, from ./SeqAn-1.3/seqan/score/score_matrix.h:40, from ./SeqAn-1.3/seqan/score.h:48, ...
written 3.1 years ago by blaise.li__biostars50
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Cases where indexing is efficient for read retrieval
... There's a nice discussion about how to efficiently retrieve a selection of reads from a fastq file here: https://www.biostars.org/p/10353/ The efficient solutions proposed in that discussion seem to be based on a read-by-read parsing of the fastq file and testing whether the read belongs to the set ...
read fastq speed database index written 3.7 years ago by blaise.li__biostars50 • updated 7 months ago by Biostar ♦♦ 20

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