User: Swimming bird

gravatar for Swimming bird
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2 months ago
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2 years, 5 months ago
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Posts by Swimming bird

<prev • 32 results • page 1 of 4 • next >
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Comment: C: CRISPR/Cas9 screen analysis: reads R1 and R2 mixed
... No, there is a mixing because R1 files contain R2 reads. ...
written 8 weeks ago by Swimming bird20
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Comment: C: CRISPR/Cas9 screen analysis: reads R1 and R2 mixed
... I don't know because the sequencing was commissioned but I think it could be due to the ligation: https://seekdeep.brown.edu/illumina_paired_info.html ...
written 8 weeks ago by Swimming bird20
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CRISPR/Cas9 screen analysis: reads R1 and R2 mixed
... Hi! I want to analyse data from a CRISPR/Cas9 screen (control vs. treatment) and I'm using Mageck (https://sourceforge.net/projects/mageck/). The sequencing was performed using Illumina (paired-end). The problem is that I've noticed that in R1 fastq files the half of the reads containing the sgRNA ...
crispr screen reads illumina sequencing written 8 weeks ago by Swimming bird20
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Comment: C: Mageck pathway command
... Anyone knows how to do it? ...
written 3 months ago by Swimming bird20
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Mageck pathway command output error
... I want to do a pathway enrichment analysis (GSEA method) by using the gene ranking file generated by the Mageck test command and a GMT file. This type of analysis can be performed by using the Mageck pathway command: mageck pathway --gene-ranking rank.txt --gmt-file file.gmt -n name Firstly, t ...
pathway mageck gsea written 5 months ago by Swimming bird20 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: Extract gRNA sequence using cutadapt
... Yes. that's the problem but I took a look to the guide and I didn't find any option to do what I want to do. ...
written 9 months ago by Swimming bird20
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Comment: C: Extract gRNA sequence using cutadapt
... This code works (it finds the sequences) but it removes the gRNA sequence... I would be grateful if you could answer again. ...
written 9 months ago by Swimming bird20
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Comment: C: Extract gRNA sequence using cutadapt
... The problem is that I have to analyse data generated by 60,000 gRNAs (all of them have to be searched in each fastq). Is it possible to do it with that number of gRNAs? ...
written 10 months ago by Swimming bird20
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Extract gRNA sequence using cutadapt
... I want to analyse data from a CRISPR/Cas9 screen (control vs. treatment) and I'm using Mageck (https://sourceforge.net/projects/mageck/). Mageck calculates the trim length of reads automatically but in case the trim is variable the program recommends the user to use cutadapt. I used cutadapt to rem ...
crispr trimming cutadapt sequencing written 10 months ago by Swimming bird20
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Comment: C: Coverage table and exons (MySQL)
... In case there are 3 exons I suppose there will be 3 different records in the coverage table, right? Do you know any example of a database that store coverage data? I couldn't find any. ...
written 15 months ago by Swimming bird20

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Popular Question 9 months ago, created a question with more than 1,000 views. For Computing ROC curves without scores

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