User: ieie

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ieie0
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Posts by ieie

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Alignment with BWA and SAMtools
... Sorry to get into the post, but this is actually a problem that I am also facing. If the quality checking was done and reference is correct (double-checked), is there a way to increase the percentage of reads that get mapped? ...
written 7 days ago by ieie0
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Comment: C: bcftools consensus sequence shorter than reference
... If I understand the format correctly probably yes, as I have a lot of positions where there is this > INDEL;IDV=19;IMF=0.904762;DP=21;VDB=0.209342;SGB=-0.69168;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,13,6;MQ=60 GT:PL 1/1:255,57,0 ...
written 11 days ago by ieie0
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bcftools consensus sequence shorter than reference
... Dear all, I am trying to get the consensus sequence of a genome using: ~/samtools-1.3/samtools mpileup -Ou -f REF alnsorted.bam | bcftools call -mv -Oz -o 1aln_paired.vcf.gz tabix aln_paired.vcf.gz cat REF | bcftools consensus aln_paired.vcf.gz > consensus_paired.fa I actuall ...
genome bcftools written 11 days ago by ieie0
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Comment: C: bcftools consensus does not produce an output
... I am using bcftools 1.9. ...
written 20 days ago by ieie0
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bcftools consensus does not produce an output
... Hi everybody I am trying to get a consensus sequences with bcftools with this commands: bcftools mpileup -Ou -f reference.fa alignments_sorted.bam | bcftools call -mv -Oz -o calls.vcf.gz tabix calls.vcf.gz cat reference.fa | bcftools consensus calls.vcf.gz > consensus.fa I then get ...
genome bcftools written 25 days ago by ieie0 • updated 23 days ago by Kevin Blighe25k
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... about variant calling, after sorting I followed the pipeline of the page you gave me and I get a (consensus sequence with the reference genome header, don't know why) and when in the end I run : cat ~/DNA-Mark/Guibourtia_leonensis_Cp.fas | bcftools consensus calls.vcf.gz > consensus.fa I g ...
written 29 days ago by ieie0
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... Right! I run the bwa mem and I got the SAM file, then I thought to convert it in BAM before sorting, thanks a lot! ...
written 29 days ago by ieie0
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... hi I am doing the sorting of the bam file through: samtools sort 103308_1116_S42_L007_R2_001.bam > 103308_1116_S42_L007_R2_001sorted.bam but I keep getting this output: head 103308_1116_S42_L007_R2_001sorted.bam ?BC?EN? ?0???~b????i???`??%?:f?R? A??O6{??p??8 ...
written 29 days ago by ieie0
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... thanks for your answer! I guess my main issue is that after obtaining the output.sam files of my series of reads.fastq I would like to end with a fasta multi alignment file containing the constructed cp genomes and I have looked for a pipeline to do that but with no useful solutions. so I after pe ...
written 4 weeks ago by ieie0
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... thanks a lot for your answer, really useful! ...
written 4 weeks ago by ieie0

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