User: omer.k

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omer.k20
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Posts by omer.k

<prev • 33 results • page 1 of 4 • next >
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Comment: C: Installing Bedtools with Cygwin fails.
... Thanks, will consider, but this is what I have to work with currently. Still hoping someone encountered and troubleshooted through this problem. ...
written 8 weeks ago by omer.k20
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Installing Bedtools with Cygwin fails.
... I haven't been able to properly install bedtools with Cygwin (Win 7), base off of the native [instructions][1]. I searched online and [found][2] that it might be usefull to reinstall Cygwin with a few extra packages. I've done so and re-attempted `make clean`, and then `make`, but no cigar. I re-run ...
bedtools cygwin written 8 weeks ago by omer.k20
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Comment: C: Extracting specific sequences from FASTQ using Seqtk
... Filtering by `grep` was successful. I used `$ grep -f name.txt -A 3 your.fq > seq_you_need.fq` as suggested by genomax. Thanks. ...
written 9 weeks ago by omer.k20
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Comment: C: Extracting specific sequences from FASTQ using Seqtk
... Thanks, I've read online and used exactly this command (`cut`) to process the lines. Now I have a file with only the unique identifiers, which will guide the filtering of the FASTQ file. Will update. ...
written 9 weeks ago by omer.k20
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Comment: C: Extracting specific sequences from FASTQ using Seqtk
... Hi genomax, How would you extract though only the ` 084b5b69-e819-426f-9ff3-fea4891af330` from a line such as `1123 084b5b69-e819-426f-9ff3-fea4891af330 runid=d20680f0495125cc465d6a96efb49b194cb0777b read=2290 ch=184 start_time=2018-03-27T11:36:09Z`? Or even from `084b5b69-e819-426f-9ff3-fea4891 ...
written 9 weeks ago by omer.k20
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Comment: C: Extracting specific sequences from FASTQ using Seqtk
... Thanks Wouter, I understand your tip. However, what would be a fast way to filter the file which contains all the reads of my interest (that is, the file which I'd liketo guide the filtering of the FASTQ file), and keep just the identifiers, i.e. `084b5b69-e819-426f-9ff3-fea4891af330`? ...
written 9 weeks ago by omer.k20
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Comment: C: Extracting specific sequences from FASTQ using Seqtk
... This is indeed nanopore data. Could these spaces in the header of the nanopore data be the reason for the error I'm getting (see my reply to Bastien's suggestion)? ...
written 9 weeks ago by omer.k20
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Comment: C: Extracting specific sequences from FASTQ using Seqtk
... Thanks @Bastien. But I have tried it before and it gives an error: [ERRO] fastx: invalid FASTA/Q format Any idea why this happens? ...
written 9 weeks ago by omer.k20
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Extracting specific sequences from FASTQ using Seqtk
... I have a large fastq file containing NGS sequences. Using prior tools I've been able to narrow down the names of some 2,500 reads which are of interest to me, in OutputFile.txt. In this file there are names of the reads ordered in the following patter: 1123 084b5b69-e819-426f-9ff3-fea4891af330 ...
seqkit written 9 weeks ago by omer.k20 • updated 9 weeks ago by genomax59k
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Comment: C: Variant calling: Samtools QUAL from NGS data Vs. Sanger quality score
... Thanks for the elaborate answer Devon. True, MinION data is generally less accurate, but this is also why I've filtered them (average Q score > 7) prior to alignment, and obviously, as you've mentioned, there are tens, sometime 100's of thousands of reads which are aligned against the reference. ...
written 3 months ago by omer.k20

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