Hello NGS community,
I'm new to NGS analysis. I have some chipseq data for a transcription factor. The sequencing facility provided data as CRAM files. I did conversion to BAM and tried to do the downstream analysis but for every conversion I was getting problems. So i decided to go from CRAM to FastQ, do the alignment and then do the analysis. I have tried the following command line, however, all my reads fail to align. Is it because the parameters are too stringent or there's something I am missing?
fazal@fazal-Precision-T1700:/media/fazal/backup/BCL11A/FastQ_Files$ bowtie -m 1 -S --chunkmbs 10000 /media/fazal/backup/BCL11A/Bowtie_Indices/human_g1k_v37.fasta -1 18418_2#1_1.fastq -2 18418_2#1_2.fastq > /media/fazal/backup/BCL11A/Sam_from_FastQ/18418_2#1.sam
# reads processed: 40095362
# reads with at least one reported alignment: 736 (0.00%)
# reads that failed to align: 40094535 (100.00%)
# reads with alignments suppressed due to -m: 91 (0.00%)
Reported 736 paired-end alignments to 1 output stream(s)
Any help will be highly appreciated.
Thank you very much!
Fazal
I'm new to NGS analysis. I have some chipseq data for a transcription factor. The sequencing facility provided data as CRAM files. I did conversion to BAM and tried to do the downstream analysis but for every conversion I was getting problems. So i decided to go from CRAM to FastQ, do the alignment and then do the analysis. I have tried the following command line, however, all my reads fail to align. Is it because the parameters are too stringent or there's something I am missing?
fazal@fazal-Precision-T1700:/media/fazal/backup/BCL11A/FastQ_Files$ bowtie -m 1 -S --chunkmbs 10000 /media/fazal/backup/BCL11A/Bowtie_Indices/human_g1k_v37.fasta -1 18418_2#1_1.fastq -2 18418_2#1_2.fastq > /media/fazal/backup/BCL11A/Sam_from_FastQ/18418_2#1.sam
# reads processed: 40095362
# reads with at least one reported alignment: 736 (0.00%)
# reads that failed to align: 40094535 (100.00%)
# reads with alignments suppressed due to -m: 91 (0.00%)
Reported 736 paired-end alignments to 1 output stream(s)
Any help will be highly appreciated.
Thank you very much!
Fazal
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