User: bandanaschapagain

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4 years, 7 months ago
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b****************@gmail.com

Posts by bandanaschapagain

<prev • 85 results • page 1 of 9 • next >
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Comment: C: Samtools depth to get the read depth
... I found the error. It was the RG I was missing up, and it just printed header to my bam file. Now, I am able to run samtools depth. Thank you. ...
written 1 day ago by bandanaschapagain30
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Comment: C: Samtools depth to get the read depth
... -I did install latest version of samtools: samtools --version= samtools 1.11 Using htslib 1.11 Then I tried to split the original .bam file by using one sample samtools view -h -r Sampl1 input.bam > Sample1.bam Then I used samtools depth -a -H Sampl1.bam -o Sample1_bam ...
written 8 days ago by bandanaschapagain30 • updated 8 days ago by GenoMax96k
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Comment: C: Samtools depth to get the read depth
... Hi, Knowing that -H option is not so important as it is for header, I just ran the code without it. for RG in SAMPLE; do samtools view -u -r ${RG} input.bam | samtools depth -a -o {RG}.depth.txt; done Now the error I have is: depth: invalid option -- 'o' Is it because of the old version of sam ...
written 9 days ago by bandanaschapagain30
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Comment: C: Samtools depth to get the read depth
... Hi @GenoMax samtools that I have is of 1.3.1 version. I see: samtools 1.3.1 Using htslib 1.3.1 ...
written 9 days ago by bandanaschapagain30
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Comment: A: Samtools depth to get the read depth
... Hi, I highly appreciate any help at this point. ...
written 10 days ago by bandanaschapagain30
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Comment: C: Samtools depth to get the read depth
... Hi @Pierre Lindenbaum I did as per your suggetion, and I got the error as depth: invalid option -- 'H' So I changed my code to parse just one sample. But I got the same error. My code for one sample is: for RG in Sample1; do samtools view -u -r ${RG} input.bam | samtools depth -a -H -o {RG}.dep ...
written 10 days ago by bandanaschapagain30
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Samtools depth to get the read depth
... I am using samtools depth to get read depth at each position from the bam file which I have after doing alignment. I used the command: samtools depth -a -H input.bam -o output_duplicates Since my bam file comprise more than one sample, how samtools depth will calculate the read depth? The output f ...
rna-seq sequencing written 13 days ago by bandanaschapagain30
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Comment: C: bcftools variant calling
... Hi, I am still not clear with what statistics bcftools used for variant calling. ...
written 27 days ago by bandanaschapagain30
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Comment: C: bcftools parameter to define mitochondrial heteroplasmy and haploid condition.
... I highly appreciate any suggestion at this point. ...
written 28 days ago by bandanaschapagain30
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bcftools parameter to define mitochondrial heteroplasmy and haploid condition.
... Hi, I am trying to analyse my mitochondrial data set. As mitochondria are heteroplasmic and haploid, while using bcftools how can I specify both? Earlier I used the command to call the variants to my bcf file created my using bcftools mpileup bcftools call --ploidy 1 -m -v -o my_input_raw.bcf I tr ...
assembly snp rna-seq sequencing written 29 days ago by bandanaschapagain30

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Popular Question 2.6 years ago, created a question with more than 1,000 views. For To get fasta header
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Popular Question 2.6 years ago, created a question with more than 1,000 views. For Downloading SRA Reads
Popular Question 2.6 years ago, created a question with more than 1,000 views. For For RNA seq data analysis
Popular Question 2.6 years ago, created a question with more than 1,000 views. For for blastp output
Popular Question 2.6 years ago, created a question with more than 1,000 views. For To make the reference index for bowtie alignment.
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Popular Question 2.6 years ago, created a question with more than 1,000 views. For How to get percentage of reads mapped to each Reference Genome
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Popular Question 3.2 years ago, created a question with more than 1,000 views. For To make the reference index for bowtie alignment.

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