User: macielrodriguez2

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Posts by macielrodriguez2

<prev • 32 results • page 2 of 4 • next >
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Filtering BAM file to extract PE reads that mapped as proper pairs, including PE reads that did not map, but their mate did
... Hi! I'm working on the assembly of a chloroplast genome. I have a bam file and I wanted to: 1. Remove pairs that did not map to the reference genome 2. Keep reads that are mapped as proper pairs 3. Keep reads in a pair where one read mapped but the other did not (I want to include the unmapped ...
assembly next-gen alignment written 15 months ago by macielrodriguez230 • updated 15 months ago by finswimmer13k
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Comment: C: Inverse mutation: Is Mummer output conclusive proof of inversion
... Also following the post. I'm wondering if the blue lines are reverse complement matches in my dot plot: ...
written 15 months ago by macielrodriguez230
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Comment: C: Selecting Random Pairs From Fastq?
... Thank you ningyuan.sg :) ...
written 15 months ago by macielrodriguez230
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Comment: C: Need help using ABACAS
... I'm also assembling a chloroplast genome and in the process of doing scaffolding. I'm now trying to resolve the inverted repeat region that was generated, colapsed into one. Thanks for the advise, I'll try chromosomer too. ...
written 16 months ago by macielrodriguez230
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How to know if the orientation of a fragment in a genome assembly is correct
... Hi everyone! I'm pretty new to the field of bioinformatics so, in advance, I apologize for the silly questions that I'll probably make xD My task is to assemble the chloroplast genome of purple maize. To do that, I'm using the really helpful NOVOPlasty assembler :D The assembler has given me a f ...
genome assembly chloroplast genome written 16 months ago by macielrodriguez230
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Comment: C: Selecting Random Pairs From Fastq?
... Thank you for your answer. I thought that the seed number have some influence in the number of reads. So using as a seed number 100 (or 4, like my teacher did in an example) should not matter, as long as i use the same seed number for both fastq files? ...
written 16 months ago by macielrodriguez230
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Comment: C: Selecting Random Pairs From Fastq?
... Hi! I have two fastq files, each with 2522553 reads in them. I want to do a sub sampling to have only 46485 reads in each fastq file, so I was thinking of using seqtk with the following commands for each fastq file: seqtk sample -s100 cp_trim_1P.fq 46485 > cp1.100cov.fq seqtk samp ...
written 16 months ago by macielrodriguez230
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... Thanks!!! I'll look for another tools :) genomecoverage from bedtools looks good too. I'll try that one. Thanks for the advice! ...
written 17 months ago by macielrodriguez230
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... Hi! I used this R code with Rsamtools with my bam file and the result was: 6503.159 What could have gone wrong? ...
written 17 months ago by macielrodriguez230
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... I ran: samtools depth zm_cp.bam | awk '{sum+=$3} END { print "Average = ",sum/NR}' and the result was: Average = 6495.19 :O is this okay? ...
written 17 months ago by macielrodriguez230

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