User: micro32uvas

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Posts by micro32uvas

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Comment: C: BWA-mem alignment is not giving desired output
... now that i am trying with .fa indexed file. Here is the next error, that needs to be resolved: [E::bwa_set_rg] the read group line is not started with @RG and here is my read group: @A00234:29:H5LTLDMXX:2:2488:31855:37059 1:N:0:GCTGGTTA I read all the "passing a variable to the read group ...
written 5 days ago by micro32uvas0
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Comment: C: BWA-mem alignment is not giving desired output
... It just includes the intermediate processes. ...
written 5 days ago by micro32uvas0
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Comment: C: BWA-mem alignment is not giving desired output
... I am indexing the genome again with bwa. However, the command that you indicated; isnt it the same as i mentioned above? bwa mem -t 24 -M ref.fna trimmed-files1/1P.fastq trimmed-files1/2P.fastq >sample.sam 2> mem-pe.log Kindly elaborate it a little. I cannot get the desired output with t ...
written 6 days ago by micro32uvas0 • updated 6 days ago by genomax39k
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BWA-mem alignment is not giving desired output
... Hello, I have clean and trimmed fastq files with an average of 150nt per read. I have tried BWA aln and also BWA mem for the alignment with my reference genome. The alignment take around 2 days to process but ends u with 92kb file each time. I have changed algorithm from aln to mem, tried default ...
bwa-mem alignment wgs written 6 days ago by micro32uvas0 • updated 6 days ago by mittu160280
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Comment: C: Alignment of the partial genome sequencing
... It worked perfectly. However, now that i have this partial desired mapped sequence, how can i look for the potential snps?? I can call SNPs but what about annotation. I am not clear about what possible should be done afterwards. I know its little out of this initial questions' scope, but it is jus ...
written 5 weeks ago by micro32uvas0
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Comment: A: Alignment of the partial genome sequencing
... I have created a bam file using bowtie2. Ref file is chr1 of the reference genome. with 2 mate pair fastq files. here is the same result: >@HD VN:1.0 SO:unsorted @SQ SN:NC_006088.4 LN:196202544 @PG ID:bowtie2 PN:bowtie2 VN:2.1.0 SRR455103.1 83 NC_006088.4 90 ...
written 5 weeks ago by micro32uvas0
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Comment: A: Alignment of the partial genome sequencing
... yes, infact, I have a specific location to align that is associated with my trait of interest e.g. 1:67,246,039- 67,350,164. And I have raw mate pair fastq files. ...
written 5 weeks ago by micro32uvas0
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Alignment of the partial genome sequencing
... Hello, I have a pretty basic question. I hope to get help in this matter. We did this whole genome targeted sequencing earlier. Now we need only a partial chr1 sequence aligned with the reference genome, instead of doing the alignment and mapping all over again. I took chr1 of the ref genome as a ...
next-gen alignment sequencing written 5 weeks ago by micro32uvas0 • updated 5 weeks ago by Antonio R. Franco3.4k
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Comment: C: Validation in paired end data alignment
... I doubt that, I got paired end data, mapped both reads with 99.14% coverage. Here's the flagstat of he data 253528473 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 251345729 + 0 mapped (99.14%:-nan%) 253528473 + 0 paired in sequencing 126740748 + 0 read1 ...
written 6 months ago by micro32uvas0
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Validation in paired end data alignment
... Hello Everyone! I am dealing with whole genome reseq data from Illumina platform for paired end data. Here's the flow,I've been following: 1. Fastq-->Sam (BWA mem with -M switch) 2. Sam-->Bam (Samtools view -b -S with F-2308 switch, which just didnt worked out for mate pairs, so i shifted ...
picard alignment samtools view -f2304 written 6 months ago by micro32uvas0

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