Hi everyone, I am new in the field of bioinformatics. I have generated RNA Seq data, my sequencing was run on NextSeq with single end reads. I have 4 fastq files per sample and therefore need to combine these 4 files into one file. I have used the cat command in linux to combine these four files into one. But when, I am using the combined file for mapping it is throwing the error. (showing that file is not in proper fastq format for mapping). Does anyone has experience on combing these file and using them for mapping?. Or can I map these files separately.
Thank you.
Is this from a single run (I mean a single = 1 run, not single-end) or was it four different runs?
Please show the output of
head -n 4 file.fastq
for every file. Please also say how the files are labelled once you received them.All four files are from single run.
following is the head -n5 of all four files
If this is paired end data then you need to
cat
the files in exactly the same order for both R1 and R2 reads.Please use
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when responding to existing posts to keep threads logically organized.SUBMIT ANSWER
is for new answers to original question.if you are a cat person, use
cat
in *nix and if you are a reptile person, usemerge_fastq
library.dear friends thank you for your suggestions.
I have mapped all four lanes fast files to genome separately and them 4 sam file generated in this analysis were used together for ht-seq count. Then after ht-seq it generated four gene counts in one txt file and in excel performed gene count of lane 1 + gene count of lane 2 + gene count of lane 3 + gene count of lane 4 = total gene count.
Any thoughts on this.
Thank you everyone.
Please don't post unrelated questions as answers in the original thread.
please read my question and response carefully
It looks like your question and response were indeed carefully read.
harshraje19 @ I am not sure if that is the way I would handle. Most of the aligners, for a given sample, allow the user to furnish multiple read files and use them in alignment to produce one single alignment file (SAM/BAM), followed by quantification per sample. But every one has his/her way to do the analysis.
Thank you everyone for taking time to answer the question.
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