User: samlambrechts299

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Posts by samlambrechts299

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Extract fasta files that are not empty from a directory and subdirectories
... Dear biostars, I have a directory containing a few hundred subdirectories, each containing 7 fasta files. A significant fraction of these appear to be empty fasta files. Does anyone have an idea how to extract only those fasta sequences that are not empty? Cheers, Sam ...
fasta recursively written 6 months ago by samlambrechts299130 • updated 6 months ago by ATpoint24k
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Comment: C: How to remove bam files that don't contain matching reads
... Works perfectly! Thank you! ...
written 7 months ago by samlambrechts299130
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How to remove bam files that don't contain matching reads
... Dear Biostars, I have 45 directories, each containing 2500 bam and 2500 bam.bai files. Each bam file represents alignment results from aligning (shotgun metagenomic) sequences to a reference fasta file. Many of the bam files are empty and only contain the header and no matching/aligned reads. Is th ...
bowtie2 bam samtools written 7 months ago by samlambrechts299130 • updated 7 months ago by Pierre Lindenbaum123k
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Comment: C: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
... And it works!! Thanks!!! ...
written 11 months ago by samlambrechts299130
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Comment: C: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
... Thank you. Unfortunately something changed at ncbi: warning: failed to load external entity "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=gb&retmode=xml&id=AF184218" Edit: This problem persists after I removed the windows carriage returns ...
written 11 months ago by samlambrechts299130
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Comment: C: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
... Thank you. However, this does not seem to work for large numbers of Genbank accessions (77 000). I receive the following error message: urllib2.HTTPError: HTTP Error 414: Request-URI Too Long ...
written 11 months ago by samlambrechts299130
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Comment: C: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
... Thank you. Unfortunately, it seems the xslt stylesheet doesn't work anymore 5 years later. It produces the following error: cannot parse stylesheet.xsl stylesheet.xsl:2: namespace error : xmlns:xsl: ' ...
written 11 months ago by samlambrechts299130
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Comment: C: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
... Dear Pierre, Dear Bioinformaticians, Do you know how to edit the above example use of the xslt stylesheet so that I can use an input text file with GenBank accession numbers instead of manually typing all the accession numbers like "HM789874\nJN225528" in the above example? ...
written 11 months ago by samlambrechts299130
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Comment: C: How To Replace Sequence Id'S In A Text (Tree) File With Taxonomy Strings From A
... Interesting! Seems like something I should check out, this ETE toolkit. Thank you ...
written 6.2 years ago by samlambrechts299130
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Comment: C: How To Replace Sequence Id'S In A Text (Tree) File With Taxonomy Strings From A
... Works perfectly! Thanks ...
written 6.2 years ago by samlambrechts299130

Latest awards to samlambrechts299

Popular Question 6.2 years ago, created a question with more than 1,000 views. For How To Trim An Arb Reference Database To A Specific 16S Region
Popular Question 6.2 years ago, created a question with more than 1,000 views. For How To Transform An Interleaved Fasta File To A Sequential Fasta File
Popular Question 6.2 years ago, created a question with more than 1,000 views. For How To Manually Check Your Putative Chimeric Sequences
Popular Question 6.2 years ago, created a question with more than 1,000 views. For How To Extract Sequences/Accession Numbers That Are Shared By A Number Of Fasta Files
Popular Question 6.2 years ago, created a question with more than 1,000 views. For How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numbers
Supporter 6.2 years ago, voted at least 25 times.

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