User: priscilladraj
priscilladraj • 10
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Posts by priscilladraj
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... Hi,
I have demultiplexed reads for each of my library. So each libary contains read 1 and read 1 as I used dual indexex. Hence, I combined both reads (read 1 and read 1 specific for each pool) into one fastq.gz file.
As for my reference file, I indexed the fasta file containning all my refere ...
written 7 days ago by
priscilladraj • 10
• updated
7 days ago by
lieven.sterck ♦ 8.5k
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Answer:
A: filter illumina index
... thanks I manages to resolve it demultiplexing it again bcl base caller software and it worked this time because I learned that teh Iseq reads i5 from reverse complement direction. So its my mistake of not knowing this. ...
written 7 days ago by
priscilladraj • 10
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... yes, it did help. thanks so much. I am not sure why I count not find this earlier. thanks again :) ...
written 9 days ago by
priscilladraj • 10
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... Hi,
I have a CSV file with just two columns(ref ID and ref sequence). I would like convert this to a fasta file format so that I can align my fastq file with these reference sequences. How do I do the conversion from csv to fasta? Kindly let me know please. Thanks
Pris ...
written 9 days ago by
priscilladraj • 10
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143
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... Hi,
I ran an iseq illumina sequencing on my libary. And due some sample prepration problem, I have a low concentration of my libary. Hence, after sequecing and base calling, the iseq base caller grouped all my reads (dual index, 3 pooled libary = 6 reads total) under a undetermined folder. I want ...
written 9 days ago by
priscilladraj • 10
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Comment:
C: Parse error at line.....
... Hey thanks genomax . I am still new so this small information is also useful for me :D ...
written 12 days ago by
priscilladraj • 10
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Comment:
C: Parse error at line.....
... hey thanks it worked :D
...
written 13 days ago by
priscilladraj • 10
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... Hi I am trying to convert sam file to bam file and encountered this problem . Not sure how to troubleshoot, Can someone help please as I am very new to bioinformatics
samtools view -S -b aln2.sam > aln2.bam
[W::sam_read1] Parse error at line 753646
[main_samview] truncated file.
...
written 13 days ago by
priscilladraj • 10
• updated
13 days ago by
lieven.sterck ♦ 8.5k
0
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125
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Answer:
A: analyse bam file
... Thanks I actually used samstat I was able to get the number aligned reads. I am new to Biostar too , so i didnt see this replies until today. Thanks :) ...
written 29 days ago by
priscilladraj • 10
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... Hi,
I am really new to any bioinformatics analysis. So please, if you could answer me in the most simplest form I would trully appreciate it. I have two bam files (bam 1 and bam 2) that were generated when I aligned one fastq read file to two reference sequences (ref 1 ref2) fasta format. When I v ...
written 4 weeks ago by
priscilladraj • 10
• updated
29 days ago by
wljlinksly • 50
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