User: Badh2

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Badh20
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Posts by Badh2

<prev • 7 results • page 1 of 1 • next >
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Comment: C: How to remove Bad Nucleotides represented by "N" from FASTA file by using UNIX?
... WOW!! it worked! Thanks! ...
written 3 months ago by Badh20
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Comment: C: How to remove Bad Nucleotides represented by "N" from FASTA file by using UNIX?
... Hi Genomax, I used sed 's/N//g' your_fasta > new.fa to remove all 'N' from a fasta sequence. It worked but now it has white space in the places of N's. Can you tell me how to get rid of these spaces as well? Following is how it looks like now. Thank you. >DAT1-COMP102480-C1-SEQ1-1788-1 ...
written 3 months ago by Badh20 • updated 3 months ago by genomax69k
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Comment: C: BAM file doesn't show the altered sample identifier
... Alrighty,,, I'll try that. Thanks again!! ...
written 8 months ago by Badh20
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Comment: C: BAM file doesn't show the altered sample identifier
... Hi finswimmer, Thanks for trying to help. May be my question is not clear. Anyways, I don't have different samples in one fastq file. I got demultiplexed fastq files for each sample so I didn't have to demultiplex it myself. But when I assembled all the samples together using Bowtie2 and visualize ...
written 8 months ago by Badh20 • updated 8 months ago by finswimmer11k
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BAM file doesn't show the altered sample identifier
... Hi All, I used the following python script to add sample identifier (S1R1, S1R2, S2R1, S2R2 etc) based on the adaptor combination. It did add the sample name as I needed but when I used the output files in Bowtie to get bam files, the sample identifier at the end doesn’t show up. (I used Geneious an ...
fastq bam written 8 months ago by Badh20 • updated 8 months ago by finswimmer11k
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Comment: A: Extracting specific regions from a bam file and exporting them to do a phylogene
... Hi finswimmer, Thanks for your suggestion. I just read about BEDtool ans seems like that has an option to do my task. I'll try and see. Thanks! ...
written 8 months ago by Badh20
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Extracting specific regions from a bam file and exporting them to do a phylogenetic analysis
... Hi all, I’m new to bioinformatics and coding. Therefore, any help to do the following tasks is appreciated. I have a bam file I got from running samtools for 8 samples. I viewed them in IGV and Geneious. I want to use these alignments for a phylogenetic analysis but for that I need to extract only ...
phylogenetic fasta bam samtools geneious written 8 months ago by Badh20

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