User: Sara
Sara • 160
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Posts by Sara
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... @ATpoint: I used bismark and data is from Pork. `bismark --quiet --bowtie2 --multicore 12 -n 1 /bismark_aln/genomes/ -1 bone.lane7.R1_val_1.fq.gz -2 bone.lane7.R2_val_2.fq.gz` ...
written 18 days ago by
Sara • 160
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... I have 8 samples and paired-end `methyl-seq` data for all of them. I have a serious problem with alignment of these files. when I aligned as paired-end (R1 and R2 together), the alignment rate is 4-5 % but if I align each file separately (R1 and R2 separately), the alignment rate would be at least 7 ...
written 19 days ago by
Sara • 160
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... I have `methylseq` data and used `bismark` for the analysis. but looking at the bam files, the alignment rate is only 8 %. then I checked the alignment using fastq_screen and got 70% alignment rate. do you know what could be the problem with `bismark`? ...
written 7 weeks ago by
Sara • 160
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... yes at the UMI level we have high duplication rate. ...
written 4 months ago by
Sara • 160
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... in our RNA-seq data (UMI is used) we have generated we have very high duplicate rate (after removing UMI and duplicate we would have only 10 % of the reads). can you let me know what metrices I can collect to investigate the problem?
...
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... what is the best way to compare expression for 1 gene between > 2 samples? FPKM/RPKM/TPM/CPM or log2 FC ...
written 4 months ago by
Sara • 160
• updated
4 months ago by
noahhelton98 • 0
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... I am doing pathway analysis but there a lot of tutorials so, I am looking for the correct way of doing that.
1- I got DE genes (up and down regulated)
2- filter them based on log2 of FC. only the genes with Log2FC > 1 or Log2FC < -1 are used for pathway analysis
3- I used up and ...
written 5 months ago by
Sara • 160
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... I have to use `DRAGEN` for small variant calling and generating `VCF` files. at this step I am doing `benchmarking` to see the results of that.
my colleague have done the same analysis using GATK3. then I compared the sites in my vcf file (made using `DRAGEN`) and the vcf file which was made using ` ...
written 5 months ago by
Sara • 160
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... I am trying to compare two VCF file (results of small variant calling from WES data) to get overlapping and non-overlapping regions separately. what is the best tool for this comparison? ...
written 6 months ago by
Sara • 160
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... I have some script in a folder and trying to make a `singularity` image (container) for them using the following command:
sudo singularity build production.sif /home/Desktop/test/
and here in the output on shell:
[sudo] password for john:
Building image from sandbox: /home/Desktop/t ...
written 6 months ago by
Sara • 160
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