User: neranjan

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neranjan0
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Posts by neranjan

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Comment: C: How to remove singletons in a BAM file using samtools
... Thanks for the clarification. So why is it important to remove the singleton ? (So my thinking is::: since its mate can not be mapped to the chromosome , the mapped read can not be accurately determined. ) ...
written 2 days ago by neranjan0
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Comment: C: How to remove singletons in a BAM file using samtools
... Thanks when I used the above command it gave singletons removed reads: 4549662 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 4373 + 0 supplementary 0 + 0 duplicates 4522161 + 0 mapped (99.40% : N/A) 4545289 + 0 paired in sequencing 2263971 + 0 read1 ...
written 2 days ago by neranjan0
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Comment: C: How to remove singletons in a BAM file using samtools
... Thanks when I used the above command it gave singletons removed reads: 4549662 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 4373 + 0 supplementary 0 + 0 duplicates 4522161 + 0 mapped (99.40% : N/A) 4545289 + 0 paired in sequencing 2263971 + 0 read1 ...
written 3 days ago by neranjan0
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How to remove singletons in a BAM file using samtools
... Dear All, I want to remove the singletons from the aligned bam file. Downloaded fastq files using fastq-dump --split-files SRR1517848 Then aligned the paired end fastq files, using BWA by: bwa mem hg19.fa R_1.fa R_2.fa -o SRR1517848.sam Then converted it to BAM format and **I used sam ...
singletons alignment samtools bwa written 4 days ago by neranjan0 • updated 4 days ago by finswimmer7.7k
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Comment: C: HISAT2 Indexing using annotation for Rattus_norvegicus
... found a solution to generate the index using more memory Cheers! ...
written 6 weeks ago by neranjan0
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Answer: A: HISAT2 Indexing using annotation for Rattus_norvegicus
... I think the answer is to provide more memory for the run. Thank you ATpoint. ...
written 6 weeks ago by neranjan0
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Comment: C: HISAT2 Indexing using annotation for Rattus_norvegicus
... Thank you very much, I really appreciate the help you gave me, going out of the way. I was able to download the index from the link. 1.6G Rattus_norvegicus.1.ht2 654M Rattus_norvegicus.2.ht2 1.3M Rattus_norvegicus.3.ht2 651M Rattus_norvegicus.4.ht2 1.4G Rattus_norvegicus.5.ht2 ...
written 7 weeks ago by neranjan0
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Comment: C: HISAT2 Indexing using annotation for Rattus_norvegicus
... thanks, appreciate it. if it complete successfully would like to know, how much memory did it used ? ...
written 7 weeks ago by neranjan0
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Comment: C: HISAT2 Indexing using annotation for Rattus_norvegicus
... Yes that might help me , Thank you very much for the help. I am using the files hosted by Ensembl Data Base, and using the hisat2 version 2.1.0 to build the index. Following is the SLURM script which I use to build it. I will post it, where the memory, partition and qos might change depending on t ...
written 7 weeks ago by neranjan0
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Comment: C: HISAT2 Indexing using annotation for Rattus_norvegicus
... No the node has 256GB memory and I only asked for 220GB of RAM. I never asks for the full amount since the node needs some memory to work with. In previous occasions I have only asked for 200GB. In pervious cases for the same index I have asked for 300GB of RAM where the node had 512GB of memory ...
written 7 weeks ago by neranjan0

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Scholar 6 weeks ago, created an answer that has been accepted. For A: HISAT2 Indexing using annotation for Rattus_norvegicus

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