User: macielrodriguez2

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Posts by macielrodriguez2

<prev • 29 results • page 1 of 3 • next >
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Meaning of these k-mer diagrams
... Hi! I have paired-end reads from corn that I mapped against the reference genome. I want to assembly the mitochondria genome, so I extracted only the reads that mapped against the mt of the reference. Before the assembly, I did a k-mer analysis of the mt reads and I got this: Considering this is ...
assembly alignment kmer jellyfish written 6 weeks ago by macielrodriguez220
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How to use IMAGE2 (Iterative Mapping And Assembly For Gap Elimination), recommendations of other gap filling tools
... Hi! I installed this program to fill the gaps in my assembly by local reassembly but reading the usage, I don't know where should I put the reads that I want to use to help fill the gaps. > image.pl -scaffolds scaffolds.fa -prefix 76bp -iteration 1 -all_iteration 10 -dir_prefix ite Here all th ...
assembly next-gen written 7 weeks ago by macielrodriguez220
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Chloroplast and mithocondria genome assembly with SPAdes and Tadpole, correct coverage and kmers
... Hi! I'm very new to this field, so I fear I'm making very dumb mistakes. My proccess to assembly these genomes is the following: We made a whole genome sequencing of purple maize (2x151 bp). Then I mapped all the reads agains the reference genome (10 chromosomes + mitochondria + chloroplast) using ...
genome assembly next-gen sequence alignment written 7 weeks ago by macielrodriguez220
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Comment: C: Using SPAdes for assembling mitochondrial and viral genomes
... Hi! I'm assembling a mitogenome of 569,630 bp. I'm using SPAdes with 60x coverage and k-mers 47,57,67,77. I got 46 contigs. Then I used tadpole with 100x coverage and k=100 and got 222 contigs. I think that my main problem is that I'm not using the correct values for coverage and kmers. Does anyone ...
written 7 weeks ago by macielrodriguez220
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Comment: C: Extending ends of sequences with the help of reads?
... Hi! I have two sets of reads: mit_1.fastq y mit_2.fastq and I want to use them to extend my contigs. I want to use tadpole but the parameter extra=reads.fq, confuse me. How should I put my two sets of reads? (mit_1.fastq y mit_2.fastq) Perhaps: extra=mit_1.fastq,mit_2.fastq ? Thank you in advance ...
written 8 weeks ago by macielrodriguez220
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Comment: C: Extract reads from a bam file to have two fastq files with the same number of re
... It worked great!!! Thank you so much genomax!!! But what are these reads? According to my flagstat, all my reads should be paired. Why are these reads without its mates? ...
written 9 weeks ago by macielrodriguez220
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Extract reads from a bam file to have two fastq files with the same number of reads
... Hi! I'm very new to the field of bioinformatics, in advance, sorry for the mistakes. I'm working with a bam file called zm.trim.sorted.cp.bam and I ran: samtools flagstat -@ 3 zm.trim.sorted.cp.bam I got this: 5604169 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 seconda ...
genome assembly alignment sequencing written 9 weeks ago by macielrodriguez220 • updated 9 weeks ago by genomax71k
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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 10 weeks ago by macielrodriguez220 • updated 10 weeks ago by finswimmer12k
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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 10 weeks ago by macielrodriguez220
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Comment: C: Selecting Random Pairs From Fastq?
... Thank you ningyuan.sg :) ...
written 10 weeks ago by macielrodriguez220

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