User: fiona.newberry

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Posts by fiona.newberry

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Comment: C: Missing SAM header after SOAP alignment
... I tried what was in the last thread. Hence why I have posted a new one ...
written 19 months ago by fiona.newberry80
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(Closed) Missing SAM header after SOAP alignment
... Hi, I am using SOAPaligner and soap2sam.pl to convert the output file to a sam file. I then try to convert the supposed sam file to a bam file and get this error messages [E::sam_parse1] missing SAM header [W::sam_read1] parse error at line 1 [main_samview] truncated file. This is ...
samtools soap written 19 months ago by fiona.newberry80
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Comment: C: SOAP aligner removes samfile headers
... Awesome, thank you for all the help!! ...
written 19 months ago by fiona.newberry80
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Comment: C: SOAP aligner removes samfile headers
... Thank you but this is using soap2bam, which I don't have. I don't have admin rights to add this onto my terminal ...
written 19 months ago by fiona.newberry80
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Comment: C: SOAP aligner removes samfile headers
... I have attempted to use this. For some reason my output file is different from what they say it should be. This is the format they say it should be: http://soap.genomics.org.cn/soap1/#Formatofoutput This is the format of my file: simulated.A.A.1.1217859/1 ACTAACCTTACCATAAGTATCAATCGTTGCGCCCTA ...
written 19 months ago by fiona.newberry80
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Comment: C: SOAP aligner removes samfile headers
... Soap is outputting the file in ASCII text format so using -h with samtools wouldn't bring a header because there isn't a header to begin with (Found all this out after posting the question). The problem is with the soap output file ...
written 19 months ago by fiona.newberry80
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SOAP aligner removes samfile headers
... Hi, I am using samtools to convert the sam file outputs from SOAP aligner to bam file. However, the samfiles do not have any sort of headers. Whenever I try to convert sam -> bam, an error message appears because the file is missing the headers [W::sam_read1] parse error at line 1 ...
soap samfile written 19 months ago by fiona.newberry80 • updated 19 months ago by Macspider2.9k
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Comment: C: BWA -> samtools pipe while filtering mapped & unmapped reads
... Okay, thank you. That makes sense ...
written 24 months ago by fiona.newberry80
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Comment: C: BWA -> samtools pipe while filtering mapped & unmapped reads
... Thank you. Do you mind explaining what the SEQTK= command is doing? ...
written 24 months ago by fiona.newberry80
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Comment: C: BWA -> samtools pipe while filtering mapped & unmapped reads
... I tried to do that but couldn't. I'll change my script. Thank you ...
written 24 months ago by fiona.newberry80

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