User: ngs_star

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ngs_star0
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Posts by ngs_star

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Comment: C: Did anyone manage to successfully run HLAScan and get results?
... Yes, no answer yet. ...
written 4 months ago by ngs_star0
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Comment: C: Did anyone manage to successfully run HLAScan and get results?
... Were you able to solve this problem? 'HLAscan cannot determine proper types' message I am having the same problem. ...
written 5 months ago by ngs_star0
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Comment: C: Did anyone manage to successfully run HLAScan and get results?
... Thanks I was able to download the data-set/db/HLA-ALL.IMGT. ...
written 5 months ago by ngs_star0
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Comment: C: Did anyone manage to successfully run HLAScan and get results?
... Hi. This is very basic question but I am trying to run HLAscan and getting error. $ ./hla_scan -l NS_L001_R1_001.fastq.gz -d A_gen.fasta HLA-A ERROR: wrong HLA gene I was trying to get DB for HLA-A. The documentation shows that I need DB like this. (1) DB HLA-ALL.IMGT : IM ...
written 9 months ago by ngs_star0
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Answer: A: how to change fastq header??
... Hi Ram. I googled myself for a couple of hours and I think I got it. Here is what I used. Find a line that starts with @HISEQ and add " 1:N:0:13" to the end of that line. There is a space included. sed -i '/^@HISEQ/ s/$/ 1:N:0:13/' filename.fastq the output of this command was @HISEQ:209 ...
written 9 months ago by ngs_star0
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how to change fastq header??
... Hello. I have a fastq file with this header. @HISEQ:209:C7FUUANXX:2:1101:1265:83081/1 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! @HISEQ:209:C7FUU ...
fastq header written 9 months ago by ngs_star0
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Comment: C: BWA error [bns_restore_core] Parse error reading ref.fa.amb- After and despite r
... I had downloaded the hg19 tar file from ucsc, untarred it, concatenated every fasta files into one file (ref_hg19.fa). Do you think concatenating every files would cause the problem? Should I concatenate only chr1-22, X, Y, M? How about should I download indexed hg19 file from iGenome? Where did y ...
written 16 months ago by ngs_star0
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BWA error [bns_restore_core] Parse error reading ref.fa.amb- After and despite removing spaces from my reference hg19
... I have read various threads here that suggested that the "Parse error reading exome.fasta.amb" is due to the whitespaces in my reference file hg19.fa Basically, I run and get $ bwa mem ref.fa read1.fq read2.fq > aln-pe.sam BWA error [bns_restore_core] Parse error reading ref.fa.amb I think I ...
alignment written 16 months ago by ngs_star0

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