User: shuksi1984

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shuksi198430
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Posts by shuksi1984

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Comment: C: Reference gene identification for contig ordering, when sample species is unknow
... How do I choose raw data from ENA, to find anti-microbial resistance genes and multi-loci sequence typing. Can I select human isolate containing single microorganism or multiple microorganism species? I choose "SRR1060710" for both the above task. Am I doing right? ...
written 5 days ago by shuksi198430
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Comment: C: Reference gene identification for contig ordering, when sample species is unknow
... > you can not choose a reference In the above case, if I have a human sample with E.coli, how to choose the reference? > you need to predict the open reading frames How do I do that? ...
written 6 days ago by shuksi198430
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Reference gene identification for contig ordering, when sample species is unknown
... How do I choose a reference genome to order the contigs once after being assembled? in my case, I have no information about clinical isolate of the microorganism. Therefore, based on what do I choose a reference for conting ordering using Mauve. My sample is "ERR209055" downloaded from EBI and task ...
assembly next-gen alignment written 7 days ago by shuksi198430 • updated 7 days ago by gb430
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Comment: C: Issues with mapping reads onto Reference genome using bwa mem
... bwa mem process is being redirected to nohup.sam, which will again throw error. Try to run bwa command in .sh file inside nohup. This way bwa process will be automatically redirected in nohup.out file and .sam file wont get corrupted. ...
written 20 days ago by shuksi198430
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Comment: C: hisat2 warning message dunring alignment of fasta file with reference genome
... Header and sequence are in two separate lines. ...
written 22 days ago by shuksi198430
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Comment: C: hisat2 warning message dunring alignment of fasta file with reference genome
... The command is: /tools/hisat/hisat2 -f -x /references/grch38/genome -1 /inputfile/SRR925687_1.fa -2 /inputfile/SRR925687_2.fa -S /rnaseq/SRR925687.sam First few lines of SRR925687_1.fa: >SRR925687.1 HWUSI-EAS053R_0010:2:1:1100:13816/1 GTGAGATCTTGTCTTAGNAACAAACAAANNACGANTAAAAAAAAAA ...
written 22 days ago by shuksi198430 • updated 22 days ago by jrj.healey7.6k
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Comment: C: hisa2 warning message dunring alignment of fasta file with reference genome
... Thank you for your response. Will check ...
written 22 days ago by shuksi198430
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Comment: C: hisa2 warning message dunring alignment of fasta file with reference genome
... Yes, I am sure. My command is: path/to/hisat2 -f -x /path/to/grch38/genome -1 path/to/SRR925687_1.fa -2 path/to/SRR925687_2.fa -S path/to/SRR925687.sam Two separate fasta files for "**-1 and -2**" ...
written 22 days ago by shuksi198430
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hisat2 warning message dunring alignment of fasta file with reference genome
... I ran the following command: path/to/hisat2 -f -x /path/to/grch38/genome -1 path/to/SRR925687_1.fa -2 path/to/SRR925687_2.fa -S path/to/SRR925687.sam I got following HISAT2 process statistics: > Warning: Same mate file "//path to/SRR925687_1.fa" appears as argument > to both -1 and -2 ...
software error next-gen alignment rna-seq hisat2 written 22 days ago by shuksi198430 • updated 22 days ago by singh.vijender20
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STAR indexing gets killed on its own at a particular time (while generating suffix arrays)
... I used the following command to build STAR index: /path/to/STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /path/to/star_index --genomeFastaFiles /path/to/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /path/to/Homo_sapiens.GRCh38.86.gtf The process gets "**killed**" a ...
software error next-gen rna-seq sequencing written 6 weeks ago by shuksi198430 • updated 6 weeks ago by caggtaagtat330

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Rising Star 4 months ago, created 50 posts within first three months of joining.

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