User: macielrodriguez2

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Posts by macielrodriguez2

<prev • 14 results • page 1 of 2 • next >
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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 2 days ago by macielrodriguez210
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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 4 days ago by macielrodriguez210
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... Does this also works with mpileup? I ran: samtools mpileup zm_cp.bam | awk '{print $4}' | perl mean_coverage.pl and this was the result: [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 Mean Coverage = 5107.87408859271 :O is this okay? ...
written 4 days ago by macielrodriguez210
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Comment: C: samtools flagstat result is different from samtools view result
... Sorry for the mistake and thank you for the answer. I was a little confused with my own results of flagstat: 6060680 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 6051340 + 0 mapped (99.85%:-nan%) 6060680 + 0 paired in sequencing 3032920 + 0 read1 3027760 ...
written 8 days ago by macielrodriguez210
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Comment: A: samtools flagstat result is different from samtools view result
... > 3217 + 0 in total (QC-passed reads + QC-failed reads) What represents the number 3217? The total number of reads analized? ...
written 8 days ago by macielrodriguez210
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Comment: C: Using the same reads to assemble mitochondria and chloroplast genomes
... What should I consider if my reference sequence has repetitive elements? The chloroplast reference genome has two repetitive elements, IRa and IRb. (I'm trying to assemble the chloroplast genome of the purple maize) Thanks for the recommendation! I'll try ARC too :D ...
written 15 days ago by macielrodriguez210
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Comment: C: How to extract only the alignments to the chloroplast reference genome of a sam
... Yes! I'm going to do that! thank you :) ...
written 15 days ago by macielrodriguez210
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Comment: C: How to extract only the alignments to the chloroplast reference genome of a sam
... Oh! So, it is not convenient to map my WGS paired-end reads only against the chloroplast reference genome???? I wanted to do that because I read papers in which the authors did just that (map all WGS reads against a chloroplast reference genome :O ) Thank you so much ATpoint! I'll try that right ...
written 15 days ago by macielrodriguez210
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How to extract only the alignments to the chloroplast reference genome of a sam file
... Hi! I’m pretty new to bioinformatics in linux :D My lab received paired-end reads (151 bp) of WGS of purple corn and we mapped them (using bowtie2) against the maize B73v4 reference genome (against all the 10 chromosomes, mitochondria and chloroplast genomes). They got a SAM file (zm.sam) of 371,9 ...
genome assembly next-gen alignment written 17 days ago by macielrodriguez210 • updated 17 days ago by ATpoint17k
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Comment: C: Abyss, Optimizing the parameter k, running time taking 7 days, still without res
... The 145 gb of data are of each read of the purple maize genome (ZM_R1.fastq and ZM_R2.fastq). We want to use that data to assembly some contigs of the genome of its chloroplast. But perhaps we should not do this with the whole data set... Thanks for your answer! I'll add that v=-v to the code to s ...
written 11 weeks ago by macielrodriguez210

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