Questions tagged [sequencing]
137 questions
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Using Bash to Manually Edit a Text or Fastq file
I would like to manually edit a Fastq file using Bash to multiple similar lines.
In Fastq files a sequence read starts on line 2 and then is found every fourth line (ie lines 2,6,10,14...).
I would like to create an edited text file that is…
The Nightman
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Using bwa mem and umitools together
I am trying to use bwa mem to align sequence reads to the hg19 reference but my sequences all have a UMI (Unique molecular Identifier). I used umitools like so:
umitools trim --end 5 input.fastq NNNNNN > output.fastq
This then properly appended my…
The Nightman
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Why does fastx_trimmer think that my fastq file is an unknown file format?
I have some .fastq files from an Illumina NextSeq run. Many of the sequences have poly-A tracts that complicate mapping them. I want to remove all sequences of ten consecutive A's and have been trying to do so using fastx_clipper as…
Forest
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Biopython SeqIO processing NNNNN in *.ab1 files
Thanks for your help. I apologize in advance if there is a function built into Biopython that handles this, I read the whole manual and couldn't find anything.
Goal: Read in a raw sequencing file (*.ab1) and process using…
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Grep pattern match between very large files is way too slow
I've spent way too much time on this and am looking for suggestions. I have too very large files (FASTQ files from an Illumina sequencing run for those interested). What I need to do is match a pattern common between both files and print that line…
user3272284
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Counting the number of occurrences of C in each line and outputting this number plus the total number of characters in that line
I'm new to programming and having some trouble in actually trying to find out what I need to do in the first place. Any help would be fantastic.
The problem:
I have several files in which I need to count how many "C"s there are in a given line and…
Jaysred
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Repeated sequencing based on columns value
Im really new to R so Im sorry if I dont make total sense.
I have a DF with data collected in several different areas, called STAND. I need to create a sequence for my data running from 1:3, but is has to restart the sequence when it comes to a new…
Erik
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Finding RNAs and information in a region
I want to find novel and known RNAs and transcripts in a sequence of about 10 KB. What is the most easiest way using bioinformatics tools to start with if that sequence is not well annotated in ensembl and UCSC browsers? Does splices ESTs and RNA…
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As I run the Cellranger count, I get the following error: "The argument '--fastqs ...' requires a value but none was supplied"
I am following the 10x Cellranger steps and using the same files for cellranger count. I run this from the fastq directory that contains all the PBMCs fastq files and the GRCh38 files too.
Yojet Sharma
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How to find Mutations for a reverse oriented gene(like pncA) from TB sequencing fasta file using biopython library in Python3?
To find a mutation like for S104R(from 2288681 to 2289241 for pyrazinamide), we have to first remove '-'(for stripping insertion/deletions if/any present in fasta file), then take reverse complement of it and then look for the particular mutation…
optimusPrime
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Is there any open source tools available for chimeric sequence detection?
Is there any tools for detecting and removing chimeric sequences from 16s,WGS,WTS sequences other than USearch. The alternative should be open source so that it can be used for commercial purposes.
Vaisakh Viswanath
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3 answers
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How can I sequence this MySQL table correctly
I've got a table containing a mixture of left and right shoes, some of which are waterproof.
I need to write a query to sort them alphabetically, but- when the name is the same- use the waterproof column ahead of…
Urbycoz
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Python: delinitate consecutive regions
I've got a .txt such as (tabs separated):
1 2345
1 2346
1 2347
1 2348
1 2412
1 2413
1 2414
The first four consecutive lines contain the consecutive integer values 2345 through 2348. Similarly, the last three lines contain the consecutive values…
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Logic to generate an alphabetical sequence in C#
The sequence should go like this.
A-Z,AA-AZ,BA-BZ,CA-CZ,.......,ZA-ZZ
After ZZ it should start from AAA.
Then AAA to ZZZ and then AAAA to ZZZZ and so on.
This sequence is pretty much like that of an Excel sheet.
Edit: Added my code
private…
Gagan Bodduluru
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