User: erwan.scaon

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erwan.scaon490
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Location:
Limoges - CBRS - France
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http://www.unilim.fr/r...
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16 hours ago
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6 years ago
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Posts by erwan.scaon

<prev • 62 results • page 1 of 7 • next >
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Comment: C: Is there a tool that sorts gtf files?
... > I want to add some annotations to a standard annotation gtf file and > then use the standard sorting to put the newly added annotations at > their "proper" place I had to do the same exact thing not long ago, [here][1] is the full recipe just in case it might help ;-) [1]: http://ima ...
written 26 days ago by erwan.scaon490
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Comment: C: Is there a tool that sorts gtf files?
... I assumed it would accept GTF when posting (after all GTF is "GFF2.5", which is really close to GFF3), but since you asked I did a quick check : Not knowing what your GTF look like, I took a random example : I ran the gff3sort tool on both the GTF & GFF3 of the [M16 comprehensive gene annotatio ...
written 26 days ago by erwan.scaon490
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Answer: A: Is there a tool that sorts gtf files?
... I recommand to sort with the tool "[gff3sort][1]", given that with stardard unix sort, lines with the same chromosomes and start positions will be placed randomly. gff3sort avoid this pitfall. For example : # Sort your gtf/gff & bgzip it gff3sort.pl --precise --chr_order natural fil ...
written 26 days ago by erwan.scaon490
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Comment: C: ChIP-Seq samples : FASTQ quality control
... **A)** To check if blacklisted regions have an impact, I did remove them using : Bedtools2.27.1 [Blacklist][1] bedtools intersect -v -a file.bam -b blacklist.bed It did not significantly impact the PCA (despite removing a non-negligible amount of alignments). **B)** I then tried to remove ...
written 27 days ago by erwan.scaon490
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Comment: C: ChIP-Seq samples : FASTQ quality control
... In the "*chip-seq-intro*" of the biostarhandbook, under the asked question : "*Should my ChIP-Seq aligner be able to detect INDELs?*", we can read : "*As a rule, aligners that cannot detect insertions and deletions should NEVER be used under ANY circumstances - unless no other aligner can be utilize ...
written 28 days ago by erwan.scaon490
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Comment: C: ChIP-Seq samples : FASTQ quality control
... Yes I guess I'll try MACS2 + Diffbind with 2 replicates for MAR & WT (despite 2 WT samples looking like outliers on the 2nd PCA). The issue may be that I did not filter my data ? Maybe with duplicates & blacklisted regions removed, thing would be better ? I did not bother with this because ...
written 28 days ago by erwan.scaon490
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Comment: C: ChIP-Seq samples : FASTQ quality control
... Removing MAR_replicate_2 & WT_replicate_2 because of `MAR_IP_2` and `WT_IN_2` would leave me with 2 mutant and 2 WT replicates, which may be fine. ...
written 28 days ago by erwan.scaon490
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Comment: C: ChIP-Seq samples : FASTQ quality control
... I edited the OP post with all relevant infos & a new PCA based on normalized BIGWIGs. ...
written 28 days ago by erwan.scaon490
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Comment: C: ChIP-Seq samples : FASTQ quality control
... Considering `MAR_IN_2` and `WT_IP_2` as outliers given the above PCA_plot, I did ran multiBamSummary and plotPCA again without them : One striking thing is that this new PCA seems to highlight 3 additionals outliers : `MAR_IN_3`, `WT_IN_3` and `WT_IP_3`. Those samples, like `MAR_IN_2` and `WT_IP ...
written 29 days ago by erwan.scaon490
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Comment: C: ChIP-Seq samples : FASTQ quality control
... Right, they are amongst the best samples regarding this metric on the [Q_score_plot][1]. It puzzles me that they end up being seen as outliers. Regarding `MAR_IP_2` in the [alignment_plot][2], not even the STAR run with --outFilterMatchNminOverLread 0.5 could improve it. It's the sample with the ...
written 29 days ago by erwan.scaon490

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