User: rioualen

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rioualen320
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320
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Location:
France
Last seen:
3 months ago
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3 years, 6 months ago
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Posts by rioualen

<prev • 56 results • page 1 of 6 • next >
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Comment: C: Possible reason for no peaks generated by MACS2
... Hi, You should maybe start with generating coverage files (wig, tdf, bedgraph...) and checking what your samples look like with a genome browser, see if it looks alright. As for Macs2, as it says in the error message: `Broader your MFOLD range parameter may erase this error.` By default, the mfo ...
written 3 months ago by rioualen320
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Bedtools window: getting feature from bedfile instead of GFF3 file
... Hello, I want to get features from a GFF3 file by using a bedfile and betools window. From what I understand from the documentation (![screencap][1] attached), I should get the desired result (features from B), however it seems that I get feature from the bedfile instead (file A). I'm using this ...
bedtools window written 13 months ago by rioualen320 • updated 13 months ago by Alex Reynolds27k
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GC content biases in RNA-seq data of A.thaliana
... Hello, I'm currently working on RNA-seq data from A.thaliana, and I have questions about quality and GC content. I guess it's normal to have a higher GC% in RNA-seq data than in the genome itself, since coding sequences usually show a bias toward GC. However, A.thaliana has a GC rate of 36% and my ...
gc athaliana mapping rna-seq written 16 months ago by rioualen320
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Comment: C: Extract basic info from fastq files in an efficient way?
... Oh yeah that's right, though it implies to run MultiQC in the first place. Thank you! ...
written 16 months ago by rioualen320
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Comment: C: Extract basic info from fastq files in an efficient way?
... Looks like what I'm looking for! Gonna dig into that :-) ...
written 16 months ago by rioualen320
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Comment: C: Extract basic info from fastq files in an efficient way?
... I know MultiQC is great, but I'm interested in using these numbers as variables in my pipeline :-) ...
written 16 months ago by rioualen320
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Extract basic info from fastq files in an efficient way?
... Hi, I'm looking for an easy and efficient way to get basic information from a given fastq file programmatically, like number of sequences, average sequence length, average GC%... I adapted [this code][1] but it's actually very slow for big fastq files. I was considering parsing FastQC's results bu ...
fastq fastqc written 16 months ago by rioualen320 • updated 16 months ago by h.mon23k
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Answer: A: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... In case someone else is running into this issue, using shortcuts for params names avoids the problem: `-q` instead of `--qual-threshold` and `-l` instead of `--length-threshold`, specifically. So in my case the problem was not related to my VM, but to the fact that my VM was using another version ...
written 17 months ago by rioualen320
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... I'm sorry but I'm not the one who wrote Sickle, that's why I actually need help... ...
written 20 months ago by rioualen320
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... case 'q': single_qual_threshold = atoi(optarg); if (single_qual_threshold < 0) { fprintf(stderr, "Quality threshold must be >= 0\n"); return EXIT_FAILURE; } break; case 'l': single_leng ...
written 20 months ago by rioualen320

Latest awards to rioualen

Popular Question 8 months ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 10 months ago, created a question with more than 1,000 views. For Looking for ways to download ChIP-seq datasets programmatically in a pipeline
Appreciated 13 months ago, created a post with more than 5 votes. For C: Get chromosome sizes from fasta file
Great Question 13 months ago, created a question with more than 5,000 views. For Get chromosome sizes from fasta file
Popular Question 13 months ago, created a question with more than 1,000 views. For Looking for ways to download ChIP-seq datasets programmatically in a pipeline
Popular Question 13 months ago, created a question with more than 1,000 views. For Get chromosome sizes from fasta file
Student 13 months ago, asked a question with at least 3 up-votes. For Get chromosome sizes from fasta file
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Get chromosome sizes from fasta file
Scholar 17 months ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Student 22 months ago, asked a question with at least 3 up-votes. For Differences between trimming tools: cutadapt, bbduk and sickle
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Get chromosome sizes from fasta file
Scholar 3.1 years ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Scholar 3.6 years ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans

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