User: caro-ca

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Posts by caro-ca

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Comment: C: How to assign keys and values in a directory by using python
... The problem is that instead of a variable, I want to assign keys and values to files in a directory. ...
written 19 days ago by caro-ca0
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Comment: C: How to assign keys and values in a directory by using python
... I will use Tepid which is going to map the paired reads against the reference genome. But the command for TEPID is `tepid-map -1 SRR4209894_paired_R1.fastq.gz -2 SRR4209894_paired_R2.fastq.gz -n SRR4209894 -x /../S288C/S288C -y /../S288C/S288C_reference_sequence_R64-2-1_20150113.X15_01_65525S -p 36 ...
written 19 days ago by caro-ca0
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How to assign keys and values in a directory by using python
... Hi! I want to map Illumina pair-end reads against a reference genome. I have a directory in which I only need to use the files that end with paired_R1.fastq.gz and paired_R2.fastq.gz for the paired reads. I am creating a script in which the paired_R1 are the keys and the paired_R2 are the values; ...
python for loop dictionary written 19 days ago by caro-ca0 • updated 19 days ago by Brice Sarver3.3k
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Counting reads and bases from a list of fastq files
... Hi! I trimmed my Illumina short reads, forward and reverse, by using Trimmomatic. The Trimmomatic's outputs were: paired_1 - unpaired_1, and paired_2 - unpaired_2.fastq.gz files. I want to know how big was the impact of trimming by counting the number of reads and bases of each file in my directory ...
count_reads python count_bases written 27 days ago by caro-ca0 • updated 26 days ago by cpad011212k
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Bowtie2 perl:warning:Setting local failes
... Hi! I need to work with bowtie2 by using anaconda2. However, I got retrieved this message: bowtie2 -h perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_PAPER = "en_US.UTF-8", LC_ADDRE ...
#bowtie2 linux written 4 weeks ago by caro-ca0 • updated 4 weeks ago by Antonio R. Franco4.3k
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Comment: C: MUMmer alignments: Trying to understand the average identity result
... Hi! Thank you for your answer. Actually, I am dealing with that coverage value. What is low or high coverage to overcome systematic Nanopore errors? Could you suggest me a paper which clarifies this? The one I read is from 2015. Thank you! ...
written 9 weeks ago by caro-ca0
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Comment: C: MUMmer alignments: Trying to understand the average identity result
... Thank you! To assess my assemblies I used QUAST, Tapestry, BUSCO and dnadiff from MUMmer, but I will pay a close look at D-genies! Thank you for your answers ...
written 9 weeks ago by caro-ca0
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MUMmer alignments: Trying to understand the average identity result
... Hi, community! I am *de novo* assembling Nanopore long reads and I am comparing my draft genome assembly against the online available reference genome. First, I want to give you some details about the inputs. The reference genome used a hybrid method that compromised Illumina and PacBio; they assemb ...
de novo assembly mummer average identity written 9 weeks ago by caro-ca0 • updated 9 weeks ago by Istvan Albert ♦♦ 82k
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How does Dnadiff deal with gap penalties?
... Hi, community! For evaluating correctness, I aligned two similar draft assemblies using nucmer from MUMmer. To get the statistics of the alignment I used dnadiff. However, I do not know how the gap penalties work. I've been looking for literature, but there is nothing about dnadiff. I hope you cou ...
alignments mummer dnadiff gap penalties written 9 weeks ago by caro-ca0
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Go plots in Blast2go
... Hi! I am using Blast2go and it seems very useful, however, I don't understand the results I am getting from the GO graphs. I uploaded two Interproscan files: (1) about protein-coding genes candidates, (2) effector Candidates. Both files are from the same organism. The only difference is that for fil ...
interproscan go terms blast2go graphics written 11 weeks ago by caro-ca0

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