User: ieie

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ieie0
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Posts by ieie

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Comment: C: bwa mem low depth and fluctuating plot
... Thanks a lot for your answer! what also worries me is that there many positions where the depth is 0 and I am not sure if I could fix this problem or not. I would not expect many positions with 0 depth. ...
written 11 weeks ago by ieie0
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Comment: C: bwa mem low depth and fluctuating plot
... ![depth plot][1] [1]: https://i.imgur.com/UJm72Nt.png this is the plot that I get. thanks for any help! ...
written 11 weeks ago by ieie0
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Comment: C: bwa mem low depth and fluctuating plot
... when I check the depth at each position, how many times a base is covered as I understood, I see very low depth like from 20 to 300. I thought that the more the depth the more confidence I get in my data. Plus, the plot is really fluctuating while I would expect a more stable plot without many peak ...
written 11 weeks ago by ieie0
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bwa mem low depth and fluctuating plot
... Hi all, I am using bwa mem in this pipeline bwa mem -t 12 -M -B 4 ref.fas xxx.r1.fastq.gz xxx.r1.fastq.gz > xxx.sam samtools view -h -b -S -@ 11 xxx.sam > xxx.bam samtools sort xxx.bam > xxx.sorted.bam samtools depth xxx.sorted.bam > xxx.bed Then with R, I read the be ...
bwa mem samtools written 11 weeks ago by ieie0 • updated 11 weeks ago by singh.vijender20
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Comment: C: R1 and R2 matching
... matching the reads in a way that bwa mem can find the pairs when it runs. Another thing that I don't understand is that after running: bwa -M -B 4 reference.fas x_R1.fastq.gz x_R2.fastq.gz > x.sam and then I run bwa mem only for the R1 file: bwa -M -B 4 reference.fas x_R1.fastq.gz > ...
written 3 months ago by ieie0
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Comment: C: R1 and R2 matching
... My problem is that I was thinking there was an error in bwa while trying to find the pairs. But I understand now that this messages are just saying that it skips the FF or FR orientation because there are not enough pairs but uses another orientation. thanks for your answer. ...
written 3 months ago by ieie0
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Comment: C: R1 and R2 matching
... thanks! I thought since in BWA it was not finding the pairs there was a problem with the matching. ...
written 3 months ago by ieie0
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R1 and R2 matching
... Dear all, I have a number of X_R1_001.fastq.gz X_R2_001.fastq.gz and I would to match them. I have seen a pipeline where they give this: # R1 and R2 matching with Compare.pl: for i in Filter-Cutadapt-Demul*.fastq; do perl Compare.pl -f $i -r Filter-Cutadapt-R2.fastq -of Paired-$i -or R2-Pair ...
next-gen bwa written 3 months ago by ieie0 • updated 3 months ago by genomax59k
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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 4 months 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 4 months ago by ieie0

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