User: Sara

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Sara160
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4 years, 7 months ago
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Posts by Sara

<prev • 81 results • page 1 of 9 • next >
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Comment: C: low alignment rate of methyl-seq data
... @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 Sara160
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low alignment rate of methyl-seq data
... 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 ...
alignment written 19 days ago by Sara160
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methylseq data analysis using bismark and low alignment rate
... 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`? ...
next-gen written 7 weeks ago by Sara160
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Comment: A: UMI and the reason of high duplicate rate
... yes at the UMI level we have high duplication rate. ...
written 4 months ago by Sara160
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UMI and the reason of high duplicate rate
... 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? ...
rna-seq written 4 months ago by Sara160 • updated 4 months ago by swbarnes29.6k
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compare expression for 1 gene between more than 2 samples
... what is the best way to compare expression for 1 gene between > 2 samples? FPKM/RPKM/TPM/CPM or log2 FC ...
rna-seq written 4 months ago by Sara160 • updated 4 months ago by noahhelton980
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5 follow
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correct order for pathway analysis
... 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 ...
gene written 5 months ago by Sara160
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a lot of missing variants when using DRAGEN for variant calling
... 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 ` ...
next-gen written 5 months ago by Sara160
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comparing 2 VCF files
... 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? ...
snp written 6 months ago by Sara160
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building container in singularity
... 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 ...
software error written 6 months ago by Sara160

Latest awards to Sara

Popular Question 17 days ago, created a question with more than 1,000 views. For M6A-seq and narrowpeak file
Student 23 days ago, asked a question with at least 3 up-votes. For CIBERSORT input file format
Popular Question 5 months ago, created a question with more than 1,000 views. For DE analysis using single cell RNA-seq data
Popular Question 5 months ago, created a question with more than 1,000 views. For number of mismatches for the alignment
Popular Question 8 months ago, created a question with more than 1,000 views. For DE analysis using single cell RNA-seq data
Popular Question 10 months ago, created a question with more than 1,000 views. For frequency of each nucleotide at each position in sequence
Popular Question 11 months ago, created a question with more than 1,000 views. For frequency of each nucleotide at each position in sequence
Popular Question 15 months ago, created a question with more than 1,000 views. For DE analysis using single cell RNA-seq data
Popular Question 16 months ago, created a question with more than 1,000 views. For DE analysis using single cell RNA-seq data
Popular Question 16 months ago, created a question with more than 1,000 views. For M6A-seq and narrowpeak file
Popular Question 18 months ago, created a question with more than 1,000 views. For M6A-seq and narrowpeak file
Popular Question 2.2 years ago, created a question with more than 1,000 views. For identification of adapters from fastq file.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Isolating reads from specific region from bam file
Popular Question 2.2 years ago, created a question with more than 1,000 views. For how to visualize the RNAseq data on IGV
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Isolating reads from specific region from bam file
Popular Question 2.7 years ago, created a question with more than 1,000 views. For filtering genes out from bam file using samtools
Popular Question 2.7 years ago, created a question with more than 1,000 views. For error in macs2 usage

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