User: shuksi1984

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shuksi198460
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Posts by shuksi1984

<prev • 102 results • page 2 of 11 • next >
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standalone blast output to excel
... I want the standalone blast output in a specific format, which needs to have only aligned sequence the corresponding sequence id . Hence, is it possible to dump standalone blast output to excel? ...
genome alignment sequence written 23 months ago by shuksi198460
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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 23 months ago by shuksi198460
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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 23 months ago by shuksi198460
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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 23 months ago by shuksi198460 • updated 23 months ago by gb1.9k
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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 24 months ago by shuksi198460
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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 2.0 years ago by shuksi198460
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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 2.0 years ago by shuksi198460 • updated 2.0 years ago by Joe18k
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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 2.0 years ago by shuksi198460
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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 2.0 years ago by shuksi198460
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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 2.0 years ago by shuksi198460 • updated 24 months ago by singh.vijender30

Latest awards to shuksi1984

Centurion 21 months ago, created 100 posts.
Rising Star 2.3 years ago, created 50 posts within first three months of joining.

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